My idea would be to have random wind velocity vector set at map start that consists of an x and y component. No z component(vertical axis) to keep it simple. This then would be used in the trajectory calculation, causing a slight change of the projectile path. However this would happen within buildings, behind hills, etc. as well or else it would become too complex. Maybe players could be able to use a hotkey that tells them from what direction the wind comes.
However all this can't be done without WSE and a very, very bored cmp.