Joker's hax is universal+ via being directly powered by the same power that gave
Big Baddie the ability to mindhax everything in the physical and cognitive universes, and works on characters that can resist that same level of mindhax. Bowser's resistance is incomparable because he has no resistance feats on that level. Thus,
they get plowed through.
Joker's deathhax is one of his go-to spells, since the Curse element is his signature. The same applies to his debilitating ailments. Joker also resists power nullification since that's one of the ailments in P5 that are backed up by the power noted above. Resurrection just forces him to incap.
Time slow barely matters since it's resisted and most of Joker's stuff is AOE, all of his magic is thought-based, and he doesn't have to worry about hitting himself when spamming death spells all over the place. If Bowser gets close, he gets nailed by omnidirectional AOE around Joker. If Bowser stays still, he gets nailed by the spells manifesting at his location. Even moving around doesn't guarantee he doesn't get grazed, and that's all Joker needs for most of his hax to work.
Even if Bowser somehow dodges all of that, if he so much as touches Joker, he gets inflicted with Fear via Evil Touch. If he so much as looks at Joker, he gets inflicted with Fear via Evil Smile. Once he's afraid, he'll die to Ghastly Wail as long as he hears it.
Once Bowser resurrects and Joker figures he can't be killed normally, he'll resort to ailments.
- Dazzler will screw up his movements by making him severely dizzy, making it even harder to dodge everything and it only needs to be seen to work.
- Lullaby puts Bowser to sleep simply by being heard.
- Makajamaon makes Bowser forget how to fight.
- Joker speaks Ominous Words and Bowser suddenly wants to kill himself.
All of Joker's spells are thought-based activation and he can at least double his thought speed via Third Eye. Most of his go-to hax are either AOE or travel through sight or sound. How does Bowser make it through all of that?