A game's code can be submitted to a repository on release to the public to be stored for the sake of preservation. The repository can always be made access on a case by case basis, thus preventing the loss of code and culture while also protecting the IP holder's rights
Apparently it's not even Nintendo, but trolls. Just that this is such a Nintendo thing to do that GMod doesn't want to even risk it
EDIT: So the domain is owned by MarkMonitor, a service that monitors for copyright infringement and sends DMCAs. Nintendo HAS used them before. So that clears up any confusion there