The same principle as with Roman throwing lances (pila). Roman infantrymen would throw pila before meeting enemy formations in close quarters. The idea being that the pila would be embedded so deeply into enemy shields that the they could not be easily removed and the enemy shields would became unwieldy. The Romans added some additional features to the pila to emphasize this effect, but the basic idea is that shields become more difficult to use when they've got a huge counter-weight sticking out of them. Mount&Blade doesn't allow for such precise mechanics but it can compensate by giving javalinmen a bonus against shield users.
As for the axes I'm not sure. It should be noted that not every kind of weapon exists on a comparable gradient to other weapon styles. As in, there isn't an exact parallel between weapon tiers for all weapon. Throwing axes do three things: break shields, scare two-handers, and kick a whole lotta ass. At a certain point I don't think there's much to improve upon for throwing axes, so "top tier" axes just don't exist.
