Joker favored matchup. Ganondorf hits hard, but his slow movement and attacks often leave a lot of openings for you to exploit. As long as you don't try to trade blows with him the matchup is solidly in your favor. The easiest way to play this matchup is to force the Ganondorf to approach and subsequently whiff-punish him.
Playing aggressively into Ganondorf typically leaves more openings for him to exploit than if he were the one approaching. That's not to say you should never play aggressive into him, just that there is more risk involved. It is very much possible to play aggressively against Ganondorf and still win, but it requires a deeper game knowledge from understanding yours and Ganondorf's frame data and hitboxes. However, even though playing defensive/campy is the easiest way to win, to truly understand the matchup you should learn to play it offensively as well.
Ganondorf is considered to have one of the worst neutrals in the game and Joker can certainly exploit his flaws. As Joker, you have way better mobility and pressuring tools in the form of Side-Special and Gun to force him to approach. However, he slightly outranges you and he's inarguably one of the hardest hitters in the game demanding you to respect his moves.
1. Attacks: An effective approach involves you NOT directly challenging his scary options, but rather, weaving around his moves' hitboxes with your own. For example, Ganondorf may often approach with Neutral-air which has a fat hitbox in front of him, but lacks one directly above or below him. He also doesn't have much jump height. Therefore, throwing out moves like Neutral-Air, Down-Tilt, Side-Special, etc. to hit him where he has no hitbox will work well. Another effective approach is to simply whiff-punish him, as his moves are on the slower side. It's important to note that Ganondorf's Neutral-Air and Up-Air respectively are effective moves for walling out approaches directly in front or slightly above him. This means that you have to approach/challenge him with care. Don't just recklessly rush in all the time.
2. Movements: His lack of solid OOS options makes him susceptible to cross ups and rolls. It can be pretty hard for Ganondorf to pin down opponents who move around a lot. You want to use your mobility to be just outside of his immediate threat range. This means you want to be close enough to adequately punish any whiffed moves, but not too close where you can get hit. The idea is to be close enough to make the Ganondorf feel threatened so that they feel tempted to throw out an attack in anticipation of you approaching them. However, being close enough implies that you are close enough to get hit by Ganondorf's Side-Special and Down-Special. Being ready to move in for a punish is important, but so is knowing when to simply back off; not every move needs to be punished. Instead, you can choose to drift or run back in anticipation of an impending attack.
3. Reading: It's important in all of your matchups that you pay more attention to your opponent than yourself. When you almost constantly look at your opponent throughout the game you will have slightly extra time to react to any sudden dash-type moves or projectiles as these moves tend to have some startup animation. Waiting until you see them throw out these moves in your peripheral vision might mean it's already too late to react to them. Keeping a constant eye on your opponent also makes it easier to absorb their habits and patterns. Maybe the Ganondorf frequently throws out his Side-Special or Down-Special when performing a normal ledge recovery, knowing that a move is likely to come out makes it easier to react to them.
Final Point: I will say this for pretty much all matchups; Joker does not benefit from a straightforward playstyle. Playing in an ambiguous manner where the opponent has trouble guessing your intentions is the optimal way to play Joker. Although I said that Ganondorf has a terrible neutral game this doesn't mean you should approach the matchup in an overly aggressive manner. Carelessly throwing out Dash-Attacks and the like will put you in a vulnerable position for a punish. If he wins a single neutral exchange he can easily confirm something like a grab or a Side-Special into a move or two for a minimum of 30-40%. As Joker, you only need to lose like 2 neutral exchanges and you're already at kill percent.
For whiff-punishing, this approach revolves around baiting him into whiffing an option then punishing his end-lag. You can bait him in multiple ways.
One way is by using projectiles in the form of Side-Special and Gun to force him to approach you; no one wants to stand there and take Eiha and Gun hits to the face. Unfortunately for Ganondorf, he's particulary vulnerable to projectiles as his slow ground and air speed as well as a complete lack of any anti-projectile moves means he has no choice but to approach.
Once you get him to approach you then consider which options he has at his disposal and react to what he chooses. His most frequently used options will be Side-Special, Down-B, and Neutral-Air.
Besides Neutral-Air, his two other approach options are easy to punish as they both have a lot of end lag.
Neutral-Air is not as easy to punish since it can be used both in mid-air or as he's landing, creeping towards you. Ganondorf landing with a Neutral-Air can be easily followed up with a jab which can easily snuff most of your straightforward attempts to punish him like dash grab. Rather than a direct punish, a more roundabout option like Down-Air or Neutral-Air to punish the landing is more effective. A well-timed Eiha can also catch his Neutral-Air landing.
Ganondorf's Side-Special and Down-B are other options and they are both laggy moves to whiff. Be aware that Down-B can be ledge-canceled. Essentially, he can cancel the ending lag of his move and immediately followup with a double jump or Side-Special to throw you off. Example below:
Successfully landing a move at low percents like Neutral-Air, Back-Air, Down-Air will often allow you to confirm into another move, usually a grab, leading to you having the advantage. When in this position, especially against Ganondorf, you should try and reap as much benefit as you can from this position. Needless to say, Joker does way less damage per hit than Ganondorf so in order to keep up with his damage output you're going to have to land way more hits than him. It's important to have some combos you can execute. They don't need to be overly complex, and Joker's combos aren't even that complex to begin with, just have some plan that you are comfortable executing.
Something I will say about Joker regarding every matchup is that you should be wary of being overly aggressive. Joker doesn't fare well when being too aggressive whether that means overextending in advantage or attempting to directly contest your opponent's hitbox with your own e.g. challenging Ganondorf's Neutral-Air with your Forward-Air, although the two moves look similar, Joker's hitboxes are generally smaller than that of most of his opponents.
1. One basic combo is the Down-Throw → Forward-Air → Dash-Attack. Against smaller/lighter characters this combo is about all you're really guaranteed, but against the larger/heavier characters you can get more/different combos. Even if they DI or directional Air-Dodge they might put themselves into a bad position.
2. Another combo to consider are the Down-Throw → Up-Air loops. The same caveats apply to this combo as the previous one above; Light-weights + DI heavily impact the damage output of these combos, but as Joker they're some of your best options and you have little risk of opting for either one.
Main takeaway from Joker's combos is that you are not guaranteed much. The rest of your attacks depend on how your opponent responds in disadvantage and how you respond. A lot of what goes into extending strings comes down to character experience and experimentation because weights and fall speeds heavily impacts what you can or cannot followup with.
Joker has an effective edgeguard game that will prove to be incredibly useful against Ganondorf. In short, most of the time you should be attempting to edgeguard Ganondorf when he is offstage. There are some scenarios where the angle may be too awkward or him doing the suicide Side-Special is too favorable of a trade for him where it may be better to remain on stage, but otherwise, if you have the opportunity to edgeguard you should go for it. Ganondorf's weight allows him to easily survive past 150% each stock which will result in more scary interactions with him through the course of each game. Edgeguarding gives you the opportunity to cut his stock short, and even considering the possibility of taking damage in the attempt the shot at taking an early kill is almost always worth the trade. Ganondorf's slow air-mobility will make him an easy target.
Edgeguarding Ganondorf is simple and straightforward. Any tool like Gun, Back-Air, or Neutral-Air will work well. Arsène augments your edgeguard tools, but is not necessary as base Joker already has everything he needs.
1. Gun:
Gun requires the least commitment, but Neutral-Air and Back-Air gets you so much more mileage for a bit more risk.
2. Neutral-Air:
With Neutral-Air you can simply run off stage, position yourself in the middle of where you think Ganondorf will use his Up-Special then throw out the move. It won't knock him back as far as Back-Air, but given Ganondorf's slow air mobility hitting him with one Neutral-Air could very well be all it takes to kill him.
3. Back-Air:
Landing Back-Air on Ganondorf after he's knocked off-stage yields so much rewards for relatively low risk. Whether you want to cover Air-Dodges, Double-Jumps, or drifting in, this move can handle it all. It's the hardest option to land from the previous mentioned attacks, but it's not that much harder with the added benefit of having less downtime compared to Neutral-Air. All you have to do is position yourself approximately horizontally between him and the stage then throw out the move. Given Back-Air's hitbox, you will want to be slightly below him, but being slightly above is okay. Being below him gives you the option of combining your Double-Jump with Back-Air in a rising motion to immediately correct your position if you are slightly off or in anticipation of a Double-Jump. The same can't be said if you are above him.
1. Ganondorf using directional Air-Dodge to stay just out of the blast zone makes him extremely susceptible to additional followups. Pay close attention to what the opponent does off-stage. If you notice your opponent burn their Air-Dodge that's often a good time to move in for the kill.
2. If Ganondorf uses a neutral Air-Dodge to avoid your Back-Air you can simply follow his descent and just throw out another Back-Air. Because Ganondorf has such slow air movement avoiding followups becomes a huge endeavor and requires him to blow all his resources to avoid getting hit, often times he gets hit anyways.
3. Back-Air is effective at reversing edgeguard attempts back on your opponent. This isn't unique to the Ganondorf matchup but is applicable against many other characters who try to edgeguard you.
VODS of Joker Vs. Ganondorf. Sometimes watching a full VOD and paying attention to all the small details can help give you an idea on how to approach the game. I'm not a professional player, but all the games are in Elite Smash, if that means anything.