With nukes, it makes absolutely zero difference.
Notice that in this instance, I've got 3 Uranium spare. I've just dropped a nuke on top of Genghis Khan's capital, taking off half its health.
In this second case, I have -1 Uranium left over and just dropped a nuke. It's left Karakorum with the same amount of health and the same number of citizens. It has also left the Mobile AA with 1HP in both cases, and my poor poor infantry with the same amount of HP.
Ergo, negative uranium makes no difference to nukes. I suspect it will impact on nuclear submarines, as they are a unit that hangs around (as opposed to a one-time usage unit).