This could be more a chemical mutation more then strict evolution though.
The loss of sight isn't evolution, its a side effect caused by a poison. A poison that is arguably passed on from mother to fetus while inutero?
Is there anything to suggest that if a Falmer were to carry a child to term without consuming the poison, that the child would not be born deformed?
Maybe not strict evolution but a combination?
All that was stated in the game, is that the mushrooms are the initial cause of the Falmer's blindness, and that the Dwemer made these mushrooms an essential part of their diet, to ensure the blindness of not only their current slaves but all future Falmer as well. So you would be right in saying that the poison must have affected the fetus inutero. This would apply, even if we assume for the sake of argument, that the effects of the mushrooms are irreversible, and that blindness persists, even if the poison is no longer consumed. A blind mother still wouldn't give birth to a blind child, unless she continued to eat the mushrooms during her pregnancy and in doing so poisoned her child.
I've followed the discussions on here for quite some time, and people have come up with all kinds of theories about the mushrooms, ranging from addiction, to clueless Falmer who don't know any better, but whether the Falmer still consume the poisonous fungi today is actually unclear. There are no alchemy ingredients that affect eyesight, but since skooma doesn't have any effect on the player character either, the lack of effect on us proves nothing.
What made me think that there was evolution involved, is that the Falmer don't seem to have eyes at all anymore. Just wrinkly red skin where their eyes should have been. They no longer needed eyes since they can't see anyway - if that makes sense. And as I pointed out, if the statue is an accurate representation of a Falmer, they changed in ways that can not really be explained with mere poisoning. They seem to have adapted. Longer ears, claws instead of fingernails...
Maybe the dlc will shed some light on this. I'd certainly like to know why the Dwemer poisoned them in the first place.