Say what you will about ninjas, but they're still pretty awesome.
Never really been my thing. I guess I prefer them to pirates, but amoral mercenaries who specialize in sabotage and espionage and assassination don't really do it for me. I can well believe they deliberately built up a glamour - doesn't make it true.
As for armour, who exactly is the shuriken-wielder fighting? Batman wears armour, Cap wears armour, samurai wear armour. Someone completely unarmoured is, yes, not too hard to injure.
if you get someone in an isolated area and give them a dozen or so small but incapacitating wounds, the odds are pretty good that he's a dead duck.
"Small but incapacitating"? Such... as? And you've incapacitated them to such an extent they can't attend to their own wounds? And, you know, if you've actually incapacitated someone, why wouldn't you finish them off?
if you hit close enough to the heart, you might open an important artery or something,
They're, uh, still inside the ribcage.
There is PLENTY of evidence that they used them.
Seriously, produce some properly cited evidence. Because there's not any solid evidence, it's all part of the mythos and popular belief.