You order a flight of 1 plane with 50% fuel (e.g. 400/800 liters)
When mission is analyzed (DCS) SEOW will remove 400 liters from the airbase reserves. If a human is slotted in this airplane, he can load 100% fuel = 800 liters (if loadout are free in campaign settings), but of course SEOW will remove the same amount of fuel as for AI (50% = 400 liters) and not 800.
Airbase fuel reserves are regarded as being in deep underground fuel stores, which are immune from air attack. To destroy these, you need to "demolish" the airbase.