The emulator is not named nintendo, this is the common manpage for the gb, gba, nes and snes commands. Having said that, some if not all of them are also trademarks but since the 9front system is not sold, I am not sure trademark protection really apply. I believe the point of trademark is to prevent a product to have a same name as a competing one which is not really the case here.

It does. Nintendo is able to make free products too, and trademarks are certainly about provenance. Nintendo could claim that the use of their trademark could confuse users on the origin of this free product.