Cruise missiles have been difficult to detect long before low radar observability via body shaping was introduced into airborne bodies. They were lethal then and they will be lethal today. Your military leadership is more realistic about Iran's chances of defense -- zippo -- than you are.
As for those buried nuclear weapons facilities...
MOPping Up: The USA’s 30,000 Pound Bomb
Iran cannot hit the high flying B-52, cannot find the 'stealth' B-2, and cannot find the low flying B-1. We do not need to penetrate all the way through in one hit. A few of them will do. The -2s and -52s will make continuing the nuclear weapons work next to impossible.
The one thing you do not understand about explosions is that even though the blast will always take the path of least resistance, if the bomb does not explode until it has penetrated, especially when the descent path through the matter is as deep as 60 meters, that path is simply too narrow to dissipate most of the blast's concussive effect. We can deliver a few of them into the same hole over a few days. That underground nuclear weapons facility will be disabled, if not outright collapsed.