To my knowledge the keys are just standard RSA-2048 keys. It's not illegal for a program to support RSA-2048, and it is no concern of the program or its developers where I get my keys from. I could just as easily use these keys in any other program. Even if in some foolish way they made it illegal for Yuzu to support industry standard decryption algorithms in this specific kind of program, then Yuzu would simply require the users to manually decrypt the game beforehand.
So the solution for Nintendo would be to take a risk and make their own encryption scheme?
That way just trying to support that prorietary encryption scheme in the emulator would be enough to run afoul of the DMCA.
But then, as a workaround I could see the proprietary encryption code being supported as an addon (ie: DLL file) that you can just drop in, without distributing it with the emulator itself and letting the users search for it on the digital high seas.