AFAIK the Yuzu accusations of containing code from the Nintendo SDK haven't been proven and also didn't come out until well after Yuzu had already shut down (it was drama surrounding the Suyu "devs" that tried to succeed them). The whole case was about them profiting off of their patreon and optimizing their emulator for a game that hadn't been released yet.

It's not that Yuzu used stolen code, it's that they released updates that optimized for the leaked copies of Tears of the Kingdom, and charged money for it. If they waited to release builds until after the release, or if they had been doing it for free, they probably wouldn't have been shut down. You might think this is a small difference, but it really isn't because having the binary file of a game is not the same as having the code that made the binary. Realistically, if you are good enough at reverse engineering binaries that you can figure out the code well enough to make optimizations for it in the 2 weeks that the game was leaked for before it came out, you are probably getting paid enough that steaking your income on a community-driven emulator would be unthinkable.

Either way, Ryujinx, which didn't profit like Yuzu did (and is written in a completely different programming language from Yuzu, with a completely different set of developers) still got shut down. Nintendo isn't doing it because of stolen code, they're doing it because it's an emulator that exists.