Nuclear bombers can notching their bomb only in direct attack, not in patrol mode.

The attack of the bombers to their target begins about 35 seconds prior to the dropping of the bomb.
In that time the AA is already calculated.

Therefore nuclear bombers can be shot down if enough air defense is present at the target.
Not only AA units counts, but also the air defense of all other units.

Missiles level 2 or higher can not be shot down, including nuclear missiles not. (If there's no bug... )

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Please, don't worry for my horrible english, i'm an old fucking Kraut and speak just enough, to drink beer with British soldiers in German pubs in the early seventies - simply drinking a beer and think you're in the pub, then you can read this without probs...

I do not recommend using AA to shoot down nuclear bombers. Fighters are much more reliable at doing the job.