I don’t think that there is an easy and effective way to do this because the terrain is lightmapped in the most cases. That means you have fixed lightmaps that declare what area is lit and what is not lit. You can change them as MindLink described in his lightswitch tutorial, but thats not effective with what you are planning.
I can imagine, that there is a way to have the same cloud-layer moving on the base-shader of your terrain the same way, it moves on the sky. Don’t know how much impact it has on FPS.
Please someone correct me, if I’m wrong. Maybe the q3map2 forum would have been the better place to ask.