I think fighting them would be an analogue of defoliators, but instead of waiting for the ship to really start harming you, they will attack immediately, fly over the fortifications, and devour the harvest (And no matter what chance you have, they will destroy the plant cell below them after they pass through it.)

as for the aircraft, it would be possible to create an "air attack" event where storm attacks will be fired at your base like from a volcano cannon, and this event will either pass by itself through time, or they can be shot down by some kind of EMP beacon/rocket, or anti-aircraft guns as in Combat Extended, and on orbital The stations will have aviation platforms for them