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.

that hasn't legally held up in the past, it's just the yuzu devs caved in with an out of court settlement since they'd have to deal with massive legal fees anyways iirc

don't think n64 games are even encrypted, so something like the Wii common key isn't necessary

i would direct the questions to harbor masters, as i'm not sure whether their software uses the same methods to decrypt ROMs as yuzu does. my understanding is that yuzu was targeted specifically because they were using nintendo's proprietary decrypting keys at runtime