A permanent injunction is entered against Defendant enjoining it and its members, agents, servants, employees, independent contractors, successors, assigns, and all those acting in privity or under its control from:

a. Offering to the public, providing, marketing, advertising, promoting, selling, testing, hosting, cloning, distributing, or otherwise trafficking in Yuzu or any source code or features of Yuzu

IANAL but that sounds like the court is banning those developers from working on Yuzu. I mean, you can still try to work on project that is 90% Yuzu but with another name but I feel like your lawyer would advise against that.

Who’s gonna stop them from contributing to one of the many Yuzu forks? What are they gonna do about it?

The answers are "the court system" and "have the police arrest them for defying a court order" respectively.

Nintendo would stop them. If yuzu devs want to go to court, they can continue development.

Yuzu devs could do it anonymously, but that's gl on not doxxing yourself, at risk of lawsuit.

I mean, I guess it can happen through private web communities of course. It would just enter the region of game cracks.

Also marginally possible someone reverse engineers, and puts up something unrecognizable compared to the original.

it's most likely part of the cease and desist order