A lot of people seem to see the stats and go "Whoa, these guys must be elite!" True, 1 ninja can defeat any other soldier (save for heroes), but you only have 60 ninjas while there's 200 ashigaru/160 samurai/120 ronin, whatever.
They can deploy anywhere and don't drop to their deaths as much whilst climbing walls. That's their advantage. They have high-accuracy fire bombs and unlimited blinding grenades. They're a support unit and can really assassinate generals if used well.