Being able to drop one atomic bomb per day would be far too much, I think. It should be a very unusual event that only a very skillful and experienced bomber pilot would be able to earn after a great number of successful sorties. Given the scale of things currently, it would be complete overkill to use one, but if the Cities or HQ were made much larger, it might be a useful tool.
No, I think if the bomb could be used more than once every map rotation, it would be too much. On the other hand, I would certainly be very fun. I can just see all of the players rushing to the target base just so they can watch. Somehow, I imagine that the target country's players might not even want to stop it, just for the same reason.