The ammo bunker we have is for the sake of the game I think. It's not supposed to be realistic, but instead it's just like an icon. Now, admittedly the ammo bunkers are rather fragile. Nearly any late war plane is able to take them down in one pass. The same is also true of everything else on the base. Aircraft, for instance, never depended on hangars. They had hardened revetments that made it very difficult to strafe, or bomb aircraft. Vehicle hangars were actually depots a lot like fuel and ordnance. But, again, it's for the sake of a game. If you harden these things up then it will take even larger hordes to capture a base.
Maybe it's a macho thing. We seem to be stuck in a tug-of-war between adding features that make base-rolling harder, and then we ask that it get dialed back because it's too hard.
I say leave this one alone.