Ummm... You do know that the burst missiles in AC5 have a ceiling of 5,000 feet, so anything above 5,000 ft will be safe, not destroyed?
And anyways, even if SkyEye was flying anywhere near the battle zone, I'm pretty sure that the shells from Stonehenge have a ceiling, not just a floor. They can't destroy everything above 2,000 feet, they must have some sort of blast radius that limits they're destructive power. I've also noticed that in mission 12, if you don't descend to below 2,000 feet, you don't get blown up by Stonehenge; at least, not until you've gotten closer and a cannon fires directly at you and you're killed by the shockwave. After all, the target aircraft are at a waaay high altitude, distracting the guns.
Regardless, the AWACS are surely not infallible, and if they didn't have plot shielding, they might have gotten destroyed at some point. Whatever happened to AWACS "Dunder"head? Think they got destroyed, or what?
Stonehenge does actually have a ceiling i was messing around with an X-02 trying to get to the max altitude and i started going above the blast radius at about 37k feet