They don't even know where the missile bases are to target them. Even if they know where an entrance is there is no knowing which way the tunnel leads after it goes underground. The missile bases have been specifically built to withstand bunker busting bombs. They are 100m+ deep in granite. On top of that there are over 100 of these missile complexes. Many of these are thought to be in north eastern Iran which means more time for Iran's air defenses to do their work.

The closer to the ground a nuke is detonated the longer lasting the fallout. Fallout that will go over to Pakistan and to a lesser extent India. Fallout from one nuke could kill millions in a few weeks and cause tens of millions of people to get cancer. 5 would render most of Pakistan and parts of india unlivable for years and kill tens of millions in the short term.

usa can't use nukes on Iran because they would effectively be using them on 2 or 3 other nuclear states.