No one would use submarines for the first strike in a major war unless it was to launch nuclear warheads from an unpredictable location. It would take months for them to get into position, even if the attacker had that many subs and it would reveal sub locations at the start of the conflict.

Hitting a ship with a missile is hard because they're usually out of land based radar range but if they all had their transponders on, it would be so much easier, especially since medium and long range missiles are getting increasingly more advanced. I wouldn't be surprised if state of the art recon satellites could pick up a cluster of transponders in a carrier battle group and use that data for targeting. If all an enemy did was take out our aircraft carriers, it would cripple our force projection outside of stationary military bases (which would all be hit in a first strike) and turn the navy into glorified mobile silos. The element of surprise is often the only deciding factor in skirmishes and battles between equal forces so it is paramount that giant, slow, and vulnerable fortresses don't broadcast their position.

Nukes don't work very well on ships much to the dismay of military planners.

There's a new generation of ballistic missile which might work, but they're extremely expensive, have limited range, and are rare. This idea of sinking the entire US fleet in one strike is utterly absurd.