Plot hole: Even if someone would make all nuclear powers launch their nuclear missiles and then destroy them you still wouldn't have a nuclear weapons free world as most of those nations have plenty of nuclear weapons in reserve. A lot would be even be armed and ready to go for a possible second strike.
Plot hole: Storm Shadow is disguised as Snake Eyes when captured. They still think he is Snake Eyes when transporting him to the prison. But he is still in his full body suit of armor. Doesn't really matter what prison you're going to, even so, this is the one for maximum security and houses Destro and Cobra Commander. It is not logical in the least for them to not have removed his body armor before even putting him in the prison transport, especially seeing as how easily his mask was removed when inside?