“It’s not automatically funny to make an innocent cute character evil/rude/innapropriate” really only applies if you’re being edgy and saying Mario commits violent murder and abuses his brother.
However, drawing Isabelle in a shirt that says “shut the fuck,” saying Yoshi commits tax evasion, and Kirby in the street at night holding a knife outside your house… are all really fucking funny and in those cases, it’s really not deep or worth getting mad about.
The difference comes from a sense of non-sequitur. With the first type of humor, there’s a “logical” negative connection of pessimism where people see a link between two events and automatically assume the worst. Like “Oh Mario’s powerup is a mushroom? That must mean he does the drugs. Peach keeps getting kidnapped? She must be doin THE SEX with Bowser!! Pokemon are like animals? The game is DOGFIGHTING!!!” And so on. It’s not really as funny for us because the connections made are just so cynical.
The stuff like Isabelle wearing a shirt saying “Shut the FUCK up. Biiiiiiitch!” Or Yoshi committing Tax Fraud or Kirby menacingly standing outside with a knife is funny because there isn’t a connection outside of “character is cute and their actions are not” and the extreme disonnance outside of reason between the two is so strong that it’s funny based on that non-sequitur alone. Rather than “Oh its funny because one could theorize Mario has a drug addiction” it becomes more “lol it’s Spyro but with a GUN!!” It becomes more of “haha Isabelle wear a funny shirt” and less “This character is being mean because of what has happened to her, likely due to your own actions”. It also helps that most of the “edgy” humor is stuff like drugs, alcohol, sex, and abuse while the non-sequitur are meant to be more outlandish (ironically, tax fraud is more outlandish due to context)
Anyway I know OP said it wasn’t deep but too bad my over-analyzing ass had to show up