if that becomes reality, what would ninjas in feudal japan look like?
Probably a lot like how they were in real life; disguised as peasants and servants. Ninjas didn't wear all black and carry katanas, they were a lot closer to a mercenary CIA.
Personally, I can see the Assassins having to deal with local ninja clans, politically and otherwise. Combine that with the general clusterfuck that was the Warring States period, and you have a lot of potential.
The reason they never make an Assassin's Creed game in Japan, i guess, is because there aren't many period in Japan history that involved in Freedom. A lot of people suggest that they should make a game in feudal japan, but i can't seem to find anything period in feudal japan that involved in freedom, or at the very least, balance of power. Not that it's not awesome to have a game in that period but Ubisoft got to stick with their theme. The clearest example is their newest Assassin's Creed game: Unity. Set during the French Revolution.
Which somehow failed miserably. Still, a suitable setting for another Templar VS. Assassins war. But to make the customer satisfied, they need to win, like a successful revolution for example.