Hmm, that gives us some interesting data about the decline of magic. We now know that the power decline included a decline in defensive magic, and this may be the first explicit statement of a type of magic that was capable at some point in the past that the Founders could not use. I'm sure this would be quite useful for Harry.

Also, I think this sort of thing might depend on practice on the size of the nuke by a lot. Some stone buildings in Nagasaki survived relatively intact and are still in use. On the other hand, that bomb had a yield of only around 20 kilotons of TNT. A lot of modern bombs are in the megaton range. So Hogwarts should be able to stand a chance to partially survive a small nuke simply due to the fact that it is a big castle with very thick walls. It shouldn't take that much magic to make that size nuke completely survivable. So even if Hogwarts can't survive a direct strike from a megaton weapon, maybe it should be able to survive a small nuke?

Edit: Another thought, if Dumbledore is now worried about the possible use of nukes wouldn't he try to upgrade the castle's defenses against specifically that sort of attack? It might be that very ancient powerful structures would survive a nuke because they are just that powerful, but even if that sort of general power doesn't exist in the modern time, there are still specific anti-nuke strategies that one could do. If for example one had a spell on the Hogwart's grounds which prevented explosives from detonating that would force a minimum distance for nukes to be used (since nukes need a conventional explosive to make the fission core go critical). One could get around that by having a gun type fission bomb with something other than explosives to launch the bullet (say compressed gas). This would put a severe limit on the maximum yield of the nuke and would mean that no pre-existing nuke would work. Another option would be to have some sort of pre-set transfiguration for the outer walls of the castle, so that if certain events occur the outer walls automatically transfigure into highly durable substances. Harry would probably have other ideas as well. Dumbledore should maybe be asking Harry for advice since Harry is both more creative and has a much better idea in detail what a nuclear detonation requires what the results would be.