User blog comment:Traditionalfire/Why are all Ninjas women? (In games)/@comment-1958269-20120913143754

A lot of it based on how easy it is to differentiate enemies at a distance. Easy way to do that is through silhouettes. You see a female silhouette at a distance, you'll automatically know that it's not a standard trooper type enemy.

As for the whole future ninja thing, you can thank G.I. Joe and Metal Gear for that.