IMO the first one explodes, the other two will evaporate before they are close enough to the target. Perhaps three strikes with, say, 5 minutes between them might work... even that depends on how the machinery of those bombs works under extreme radiation.
However any nuclear strike option, on part of either Israel or the USA, is politically impossible. Iran is not at war with anyone. The country that dropped the bomb and killed, say, 100,000 people and caused widespread contamination of half of the Europe and Asia would certainly be punished - by a mandatory, worldwide trade embargo, for example. The General Assembly of the UN will gladly vote for that, overruling the [stalemate in the] Security Council.
I think the statement of Ehud Barak is crafted to explain, primarily to Israelis, why there will be no strike. I personally believe that impossibility of taking the Qom site out is just one facet of the problem. Much bigger problem is that Iran can inflict an unacceptable damage to Israel in return, just using its existing, conventional weapons. Iran's missiles may be poorly built, but they have plenty of them, on mobile launchers in mountains. By the time Iran is out of missiles there will be nothing left standing in Israel.
Don't count Israel out. I've read the back of the book, and they win!
I would guess conventional deep penetrator bunker busters (by the nature of what they do) are pretty harden and designed to take a lot of G-forces and temperature before going boom. I think the follow ups would zoom right through the loose debris easier than the primary zoomed through a couple hundred feet of solid rock.