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.
C&D in Brazil stands for Comedy & Despair, where you’re the one laughing at the company desperate to get you to do what they want without having any actual legal leverage
I this is the more probable version of events.