A few things:

First, the LLC settled with Nintendo. They do not have the funds to pay their debts, now, so they'll go bankrupt. The developers won't pay a cent, likely. Maybe a bit of cash left over after paying their lawyer, if there is any, but it won't amount to much.

Second, they were being sued for damages. Just stopping something after causing damages is insufficient.

Third, this isn't a judgment, it's a settlement. That means that it was their "choice" to negotiate with Nintendo instead of going to court. In the settlement, the group agreed to cease & desist and not work on Nintendo systems at all any more, basically. ~~I haven't looked into it, and I'm not as lawyer, but again I think this is just the LLC, not the individual developers? If so, this also means basically nothing at all.~~

Realistically, developers on this team likely won't continue working on Nintendo devices, because there's nothing stopping Nintendo from just using them again and facing "actual" penalties next time. But there should be very little harm to them individually for this.

And no, nothing is stopping them from continuing to work anonymously on this project on the dark web. Nintendo could never prove it, so long as they aren't so stupid as to announce it. It would take some pretty strong evidence of continued infringement to get a search warrant, I would think, so they're likely in the clear.