I don't know, if I put out GPL software, I wouldn't give a fuck if it got used to fuck over Nintendo without following all the GPL nonsense. They took the legal risk of going up against Nintendo, I sure as hell didn't take any risk writing code. Them profiting a bit isn't the end of the world. No one was going to make any money staying within legal limits anyway, nothing was "stolen".

Edit: Just to be clear, all I know about Bowser is based on the parent comment. Maybe he's a bigger POS than the example given but, from that, doesn't seem like a major villain.