It looks to me like resupply missions don't do anything but give you perks (maybe) and damage your overall stats. I believe that the amount of repair you do should be added to your cumulative damage for purposes of calculating damage/sortie, or resupply sorties should not count against you as sorties at all.
I spent a lot of time today doing resupply runs in both goons and vehicles, and my stats only went downhill. That's no way to get people to resupply.
