The point is, when the bill of rights was written, atomic bombs weren't an apple in anyone's eye, and the second amendment doesn't account for the possibility.
I don't think that "arms" includes atomic bombs. I don't think that we can turn to the Supreme Court for answers, as the Supreme Court has only considered two gun rights cases (United States v. Miller and United States v. Cruikshank).
I don't think atomic weapons are protected under the Second Amendment either. The very definition of "arms" as the Founding Fathers meant it to be was to protect any hand-held weapon. Rifles, pistols, swords, anything that is designed to be hand-held, was meant to be owned my the public.