According to an official statement on Ryujinx’s Discord server, developer gdkchan was contacted by Nintendo and they were offered an agreement to stop working on the emulator project, and while the agreement wasn’t confirmed yet, the organization has been entirely removed.
As I understand it, cause of the country the creator is from, a C&D was unlikely to be enforceable. Money, on the other hand, is a universal language.
I think this is the more probable version of events.