The huge mountains in question could again be playing with shadow calculations. Not only is it a huge surface area which could require massive shadow calculations as a result (it's likely to be casting complex shadows even onto itself in a lot of cases and could also play hell casting them onto troops), but it is also a fairly complex surface for shadows to be cast onto from units and other things as well. Either or both of those factors could significantly drive up the amount of computational power required to accomplish the dynamic shadow calculations. I haven't personally experienced any lag on mountain maps, though, so I can't really comment on whether it appears to be due to one thing or the other, and my comments here aren't trying to win an argument, merely present possible explanations.

Thinking more on that though... I imagine trees are casting shadows about everywhere too, though I can't remember ever seeing the specific effects of that. If they do cast shadows then one might expect forests to have as much impact as a mountain does (maybe not, their surface area is still probably a lot less), if shadows are a factor in this problem. If they don't, then it still could make sense for mountains affecting shadows to be a source of slowdown.