destroying something is a good way to get rid of any excess polies in the scene when they are no longer needed. its just sort of a way to keep the game running smoothly. like if you had space debrits from all 12 waves of htl fighters. it would sorta be like a mission where all the ships jumped in at the same time.
then again not every kill results in an explosion that vaporizes everything. seriously if you blow up an 8 km long chunk of metal, its gonna leave a little bit more behind than a few relatively small chunks. and with fighters, sometimes you hit the reactor, but sometimes you takeout the pilot or the control surfaces or the thrust ports or knock out the avionics. on the other hand theres

of stuff on theese ships that if you hit them, nothing will happen. theres

of empty space in there.
there are places you can hit to destroy the ship, there are places to hit to cripple the ship, and you can also hit the means to control that ship like the pilot or the avionics. sorta like in mw2 and probibly other mech games as well where you can shoot out the cockpit (and then salvage the chassis for the next mission).
its probibly easy to script or fred in such features though.