That's on paper. It's extremely unlikely that they set an LLC with millions of dollars in assets. The reason they set up the LLC was that if they got sued they could settle for any amount, knowing that they would just declare bankruptcy and pay nothing except their legal fees (which, having settled immediately, are very low)
And that's probably why Yuzu didn't stand up to Nintendo. They probably had enough areas for Nintendo to attack that fighting it could leave the emulator community worse off if it goes to trial. Why risk the money to fight something unless you're sure you can win?
Projects like this should be self-hosted & encourage contributors to set up their own self-hosted mirrors to make sure the code is both distributed & decentralized which users/makers have full control over their platform.