Presumably forks remain public on Github at their own risk, but Nintendo may shift to a DMCA removal policy now that are about to have a judgment.
The judgment has two sections, one for people who have “privity” and more direct relationships with Tropic Haze, and another for “all third parties acting in active concert and participation with” Tropic Haze. The latter enjoins only sharing code and decryption keys. So it certainly sounds like this was drafted to capture, in the Court’s order, people who don’t have a relationship but are code-forking.
Nintendo doesn’t have nearly as clean legal leverage for randos and individuals that don’t have a company built around this emulator, but I actually predict they’ll do GitHub DMCA removals on forks based on a broad reading of the injunction.