The Plutonium bomb should t should cause any liberals staying within the safehouse where the plutonium is stored will have constant rolls against their Health, and random stat drops to represent mutation and radiation. It would require a large science skill - ~12+ to even consider this. Around $100,000 worth of equipment should be installed, and the location would automatically get +heat just for the equipment being suspicious and eating up energy.
All of these things are one-time costs, implying that preparing and creating nuclear bombs are costly and dangerous; and if you get raided unaware, everything is lost, but should work like a factory constantly producing them once fortified and immune to raids - as long as you can actually get the plutonium.
Plutonium should only available while the nuclear plants are still active, and a successful bomb should instantly change public opinion regarding it to L+. While this is good; it also makes so that these bombs aren't abused by limiting their supply.
The only really problem I have with these is - unless closed down facilities give bonuses to their respective issues, it might make the game boring - if you close down everywhere, you just might be left with nothing to do except just to sit down and wait until the facilities reopen.