The premise is, that for whatever the reason, Saddam decides to keep his nukes a secret. Maybe he wants to humiliate the USA by prompting them to invade and them using them? Saddam was never really good at looking at the potential consequences of his actions, after all.
The US has no idea Iraq actually has nuclear weapons capability. What does the president and his generals decide to do? Push on, and risk nuclear strikes on their bases, Saudi Arabia or Israel (which would, have no doubt, be politically disastrous for the US) Or do they simply withdraw, or do something else? Remember the huge hostility most of the western world - even long time allies like France and Germany - had towards the invasion in the first place, and now imagine the fallout (no pun intended) if the US decided to nuke Iraq into oblivion.
The US already has the Patriot PAC-3 deployed in theather which can intercept inbound IRBM. The Israeli's have the Arrow ABM system already deployed. The US keeps pushing forward since they are already commited to the invasion.