Ryujinx is based in Brazil, where copyright laws are a lot different and it would be almost impossible for Nintendo to sue. What likely happened is Nintendo lawyers flew out to brazil, showed up to the house of the frontman of the project with a briefcase full of cash, and all he had to do was shutdown the project, and sign a piece of paper. He took the offer, and that was it
The likely reason nintendo shutdown Yuzu/Ryu is because the Switch 2 architecture is probably very similar to the original switch, and they didnt want Switch 2 emulation available day 1. Switch 2 emulation will build on top of Yuzu/Ryu, kind of like how dolphin supports both gamecube and wii. It's the same type of thing with Yuzu/Ryujinx
When Yuzu shutdown, there was never any major development team assembled to carry a fork of the project. While forks exist, they arent in heavy development. This is because everyone said... well who cares, we can just use Ryu. Now that both are gone, and there is not switch emulator being developed at all, I think you will see a development team assembled, likely from both projects, and one of the two will be forked and carried on. Someone will pick up one of the projects and put a good development team together.
Either way, Switch 2 emulation will happen early in Switch 2 life cycle because the ground work is already laid, which will just require some tweaking. It helps that we already know what the hardware will be for the Switch 2, so it really wont be a crazy amount of work to get a Switch 2 emulator up and running within a few months of Switch 2 release