Your world is filled with photosynthetic lighter-than-air hydrogen-filled organisms. They crowd the air, moving to and fro in clouds and clusters. The basis of the ecology depends on these organisms, so simply eliminating them would be environmentally disastrous. If you combined them with yolo man's (+1) answer, these organisms might even be part of the shielding of the surface from radiation. Great flocks of birds and/or insects follow these organisms around, feeding from them. As a result, your skies are extremely crowded.
Missiles fired through this soup inevitably get gummed up, and the density of material makes non-GPS navigation almost impossible. Even air travel by fast aircraft would be almost impossible (I used a similar answer for a question about airships).
In an EMP-rich environment from a high-output star, you also answer the ICBM question at least in part. Non-electronic gyroscopic guidance systems could still be made to work even in the worst of conditions. You can make a big enough rocket to get through the atmosphere for a moon shot, or wait for a thinning of the clouds to launch, but you usually want weapons to be reliable at the time you need to use them. If you have a space program, you would likely still need to deal with nuclear weapons (even if they ended up being space-based) but these platforms would be less desirable due to the radiation.
Artillery, on the other hand, would be relatively unaffected. The accuracy of shells might go down due to interference, but bombardment would simply increase the volume of fire to compensate. Ground weapons would be competing with dirigible airship weapons, and I'm guessing long-term the ground weapons would win out.