I see no effect whatsoever from destroyed strats. Although fun to make a mission for, if they were too important it would cripple a side and make people switch to the winning side.
What Id prefer to see are plane and tank factories. The plane chosen that the factory produces is changed at random, every hour. These would be all the perked and 5.0 ENY planes. The vehicle factory would produce the Tiger. If a factory is destroyed, it stays down for 60 minutes and the plane it was currently generating is unavailable until the factory re-opens.
Also..unlike the HQ, there wouldnt be a 163 base right next door to it.