It’s also important to note that it’s not “just” the B-29 bomber that could have delivered a theoretical nuke.
I’m sure if the Russians or Germans had managed to get a nuke together, they would have used whatever bomber they had that was appropriate. Not every plausible bomber option had a cieling of 31,000 feet.
I bet a B-25 Mitchell, or a father of the night could have delivered fatboy too.
If you deny aa-fire/interceptors against the nuke bomber, you might aswell deny aa-fire against all bombers. As in Axis and Allies the piece doesn’t change.
Nukes should also be able to move 1 space on land. I’m sure if the Germans or Russians had one, they may have moved/used it in place, were things going wrong.