The original supply ships are just regular bases like all the other harbors. The only mod that I'm aware of that changes this is H.Sie's and Stiebler's work (if you want this mod to work also with the supply ships you have to change their names to 'U-...', i.e., the name must start with 'U-'. For instance, "U-supply ship Thalia"):
http://www.subsim.com/radioroom/showthread.php?t=174225
12. U-Tanker Mod - by Stiebler and h.sie
Everyone complains that, when you dock at a U-tanker in mid-ocean, you lose all your current renown/tonnage for medal purposes, you get a full refuelling, full repairs, full torpedo load-out and you lose the patrol grid which BdU ordered. No longer! With this Fix, you get only 1-4 air torpedoes, you retain the patrol grid details, you receive some repairs to your hull-integrity (but not to equipment) and you receive a fuel upgrade, of up to 30% of the full capacity.