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
They got it from a twitter post that never bothered looking up who owns the domain. The domain is owned by Nintendo of America Inc not some internet troll.