In reality those weapons don't completely ignore armor. I don't know about you, but if I had to fight someone wielding a pole-ax I'd prefer to do it wearing a full set of articulated plate . But MeG (for good and ill) doesn't have the granularity for partial effectiveness. So given a choice between anti-armor weapons having no benefit against armor, or ignoring it completely, the later is a better compromise from a gameplay perspective. But having armor is still better than none.

That said, I personally think unprotected shouldn't be a drawback (and maybe even a benefit) against elephants. The only protection is getting out of the way!