During the SNES era they did do things like no blood in Mortal Kombat but they realized that sales suffered vs the unaltered version. Then the ESRB was created so game ratings took over the responsibility of content. Rare was also given some freedom on what they could create on the N64. Just look at Conker's Bad Fur Day on the N64 and it's allowed adult language and content vs Conker on the Xbox which was censored.
The thing you're thinking of with Rockstar is actually their pre GTA days when they were known as DMA design. Nintendo forced them to make some changes to one of their games, but not for mature content.
"DMA was asked by Nintendo to join their "Dream Team" of developers for the upcoming Ultra 64 system (later renamed Nintendo 64), alongside such other developers as Rare, Paradigm, Acclaim, Midway Games, and LucasArts.
Under this arrangement, DMA would produce an N64-exclusive title that Nintendo would publish. The result of this collaboration was Body Harvest, a third-person 3D vehicular action game with a storyline about aliens arriving on Earth to harvest humans for food. Nintendo requested a number of major overhauls, such as the addition of puzzle and role-playing elements, to make the game more appealing to the Japanese market. The game underwent numerous delays, and Nintendo finally decided to drop their publishing plans. Midway picked up the rights and finally released it in 1998, almost three years after the game was first shown. Reaction was mostly favourable, in particular for the game's innovation and free-roaming gameplay, although a few gamers criticized the graphics." - source
