So yea, Dr. M is a fuck
Actually, the movie Dr M is very carefully trying to be appear less than omnipotent. The whole "99% of the warheads" thing is a complete lie, based on what he does with the glass clock on Mars. If he can keep hundreds of these parts floating in precise patterns at once, he can covertly fubar any realistic number of missile silos marked with radioactive materials over the course of a few hours. He is pointedly keeping this capability hidden to avoid giving Nixon a free hand, but his restraint and lack of scale perception also prevent him from acting spontaneously at all, explaining why he "allows" the Comedian to commit atrocities.