I agrey, counting the precice dammage you did to reduce the base/NPC to 0 hull and adding that to your dammage total would be the bedst option.
but if you look at a base after it have been disabled, you will notice that the last hit that kills it, isnt even substrated from total hull
so all bases you disable end up with 5 - 599 hull left, depending on how mutch hull it have left before the kill shoot

my bedst guess is Dan picked the easy solution, disabeling the base before putting dammage on hull and adding the dammage done to dammage scores, to prevent bases getting negativ hull and to prevent overkill - that could make it hard to change things
here is a good eksampel on what can happen when you end up with nagativ energy,
viewtopic.php?f=5&t=38503negativ hull on a base could be just as bad....
also, as I sayed, if you know how the system works, it easy to work around