Nintendo's argument in the filing is that Yuzu is designed primarily for circumventing the Switch's encryption (a.k.a. copyright protection measures). Their justification is that Yuzu uses prod.keys to decrypt various things like the ROM filesystems and the system firmware*. Ryujinx also uses prod.keys, so they would be just as legitimate of a target for that argument as Yuzu is.

Personally, I think they chose to go after Yuzu first because it's more popular and runs at playable framerates on modern Android devices. If the lawsuit goes in Nintendo's favor, I guarantee they'll immediately use that precident to make the same argument against and swiftly kill Ryujinx.

*This is actually a valid argument that is not affected by past suits like Bleem v. Sony.