There are in fact lethality values in battle_config.xml intended to model the effect of projectiles piercing flesh but not killing the target:
Code:
	<!-- global combat balancing factors -->
	<combat-balancing>
		<missile-target-accuracy>
			<infantry>0.79</infantry>
			<cavalry>0.56</cavalry>
			<elephants>0.39</elephants>
		</missile-target-accuracy>
Note: The "accuracy" descriptor above is a misnomer and actually describes lethality.

That means that a normal projectile that has hit a target and penetrated its armour and shield will have a 79% chance of removing a hitpoint if it's an infantryman, 56% if it's a cavalryman and 39% if it's an elephant.

Javelins and artillery rounds seem to ignore these values and always have a lethality of 1, which would explain why they are so effective against elephants.