GitHub link to Nintendo's claim - all the details you need are here
The emulator forks which are being taken down are as follows:
Despite this, the one fork that continues, and will continue without takedown is Ryubing - by Greemdev. This is created by an original member of the Ryujinx team. It's safe, the code is beyond reproach (and violates zero laws or Nintendo code) and actually brings helpful updates.
Still...shitty news. And more indication that the Switch 2's architecture will be damn similar to that of this current Switch. Them taking emulators down means the upcoming games have a solid chance of being emulatable on release. But...that's my own (and others') conjecture, so we'll see when the time comes.
Repos wouldn't include the keys, but they'd include instructions on how to obtain them. Those instructions (according to Nintendo's legal team) are enough to say that Yuzu violates the DMCA.