I don't know if HT considers a dead HQ a real issue or not. I remember taking out the HQ and seeing it back up before I cleared the enemy's territory making it not worth the bomber sorte even with the City mostly down.
If it truely is a problem, and somehow I doubt it, then I've always wondered why the HQ didn't have its own radar tower dropped into the terrain to warn of the initial attack.
For gameplay in the next version, I always liked the old multistage HQ model of friendly bar, enemy bar, friendly dots, enemy dots, with separate buildings and graduated hardnesses.