Most emulators have patreon or other forms of monetization. The rulings which set the precedent that emulators are legal were about commercial emulators.

I really don’t think this was about the money, instead it was about how open yuzu devs were talking about piracy and distributing copyrighted material in their discord.

I believe money wasn’t even mentioned by Nintendo. Additionally, Nintendo shuts down projects regardless of whether they make any money or are just small fan-projects for decades-old games.