Some weapon don't work for air unit atm. Shotgun, grenade, cannon shell and poison gas can. All others weapons work fine. Air units ignore collisions. So any weapon rely on collision don't work for air units.
I'll need some digging to change those in next update.
It seems the problem is related to the modded weapons. Although I attack them with modded weapons they seems immune to my attack. Can you look into it?
Or perhaps it seems to be because of targeting system of Industrial Revolution2 mod
OK. I'll do some digging on that mod. My guess is that it use custom bullet projectiles. Many of the projectiles in the base game needed some changes in order to hit air.