The Yuzu devs did quite a bit wrong. For starters they were selling access to early builds of Yuzu (making ~$30,000/month) and allegedly promoting piracy on their discord servers (specifically they were helping people play Totk before it came out last year iirc). These were the things Nintendo went after yuzu for. If they had just released their emulator for free while stating they didn't support piracy (and actually maintained that viewpoint), Just like how every other emulator does it, I highly doubt Nintendo would have ever gone after them.

If you keep your hands clean as an emulator dev and don't release any copyrighted material there's nothing Nintendo can do to you. At least that's what the past has shown.