Oh yeah, I'll agree that Yuffie isn't a very good representation of a ninja. Though really, Edge and Shadow fulfilled the role of "dark mysterious character" much more than the role of ninja; their choice of class was merely incidental. There's some kind of tendency in Japan to make dark characters ninjas by default. In FFVII, they fixed that by giving us Vincent, who's much cooler than the both of them, in part because he has the good sense to use a gun.