I see both points, but think it makes a big difference whether a nuke is inside or outside. One nuke inside a battlestar will end the fight in no time, tear it into pieces just like how the columbia blew up in the 1st war. If it explodes outside, the armor absorbs "most of the bad stuff", radiation, and energy. Still does massive damage, but is survivable.
Then next look at the construction of a basestar, its actually flimsy as hell, built to fight from far with long range missiles and use fighters to take out incoming missiles, and its shape makes for a harder target (since its less clustered and has large gaps and all). A nuke on a basestar would do massive damage and tear off at least the wing it hit. Basically one hit would probably take the basestar out of the fight for a while, two should destroy (This is all in my opinion, feel free to comment).