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.
The dev got bribed (or threatened) by Nintendo to manually delete the repo. GitHub this time didn’t do anything
Lol, why do you think payment is the more likely of the two options?
Why the hell would Nintendo pay them anything when a C&D is cheaper and just as effective.
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.