Although I do not use them, I think throwing weapons can be pretty deadly if you max the throwing weapon and power throw skill, even with the kind of damage it actually does. I mean if you stick to it you can have a proficiency of about 300 or more and be pretty accurate.
I remember in some siege battle against the empire being suddenly knocked out by a spear in the head thrown by some empire heavy legionnaire (not even an immortal) while I was shooting at their crossbowmen! (Damn, now I take those spearmen first)
And again good plate armour should protect you from being one shoot even by a javelin (except in the head or by an exceptional shooter). I mean it has some chance to get simply deviated by the armour, although if it pierces it, it should be a one shoot kill. So the actual system well represents it