Ok, the crater of an unexploded nuke is being way too big of a deal here.
Ok, I have no idea how heavy the nuke in Megaton is, but I would guess it is probably at least 1000lbs, probably more. Ok, said object is dropped from 50,000 ft, falls from space, or however the bombs were delivered in the war, its gonna make a pretty good sized hole in the ground.
Megaton itself isn't built inside the crater, it is built around the little crater around the bomb with the water pooled in it.
As for why people would build around it...I don't imagine survivors of a nuclear bombardment are too picky about what they conceive to be a sign of hope presented in the form of a bomb that didn't go boom.
Plus, no one in the town is a nuclear weapons specialist, they probably figure the bomb was a dud and presents no issue.