You’re trusting that a) they’re not malicious and b) they have their shit together and c) even though they do have their shit together someone doesn’t find a random exploit anyhow.
You could say this about literally any solution short of hand-delivering cash in person.
This is a Switch emulator, meaning these are games that are still available for sale. It’s not like taking down a SNES emulator or something Nintendo hasn’t made available for 30+ years, it’s involving games they’re selling today. Taking down an emulator is literally Nintendo protecting its IP.
If you were using this emulator, you weren’t likely purchasing anything from them in the first place. And I’m no doctor, but… I’d have to imagine that’s likely the reason Nintendo took this down to begin with.