The second amendment, being an amendment, overrides the exercise of the power granted Congress in the main body, if that power is exercised in such a way as to "infringe" on the right of the people to keep and bear arms. Prohibition certainly violates the right to keep arms, if one cannot acquire them, it's very difficult to keep them.
The same is true of Congress exercise of it's other powers in such a way as to violate the "restrictive clauses" that we call the Bill of Rights.
I agree. I am at a loss to explain why some of the federal laws (the NFA, the GCA, the AWB) were not challenged as violating the second amendment. With the exception of Miller, not one lawsuit.