I've been wondering about the same thing. I went to war with Cathy in a previous game (playing Askia) and sent in paratroopers in advance of my main force to take out her uranium mines so she couldn't build any more nukes, as she'd been going all nuke happy on Hiawatha.
Anyway, taking out her mines did stop her building nukes, but she was able to use two she already had on two of my cities. I didn't notice any reduction in damage compared to getting nuked normally, so my guess is that nukes don't suffer the 50% penalty from loosing the uranium their dependant on.
If nukes do take the 50% penalty, their damage must already be so massive that it makes practically no difference to the cities/units they explode on.
If anybody knows the answer for sure, I'd appreciate knowing
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