Wrinkles don't matter too much. Technically, there probably is a bit more drag and the aerodynamic are slightly effected, but not enough to notice except maybe on high performance planes.

Yes, weather changes will cause wrinkles to come and go. Typically after some time the covering will stabilize and the wrinkles happen less often and with less severity.

In short, minor to moderate wrinkles really don't effect a planes flight much. HOWEVER, loose edges can seriously effect flight. Be sure all seams are sealed, i.e. the covering is attached at the edges.