Metal fatigue in steel normally requires thousands of cycles - even millions - to occur.

The exception is if there is 'plastic deformation'; bending the metal beyond the elastic limit to the point it is permanently deformed. Do this back and forth a few times and the metal will break - and be weakened with each cycle. Not much plastic deformation would happened to the main hull on a deep dive.

A thin walled vessel like a sub pressure hull collapses due to the wall instability under heavy load. Technically, it is a form of Euler beam buckling, which is an elastic phenomena.

However, localized spots may be subjected to unusual stress and undergo plastic deformation, so weak spots may be weakened by too many deep dives. By weak spots I mean a local joint, seal, valve, etc.

So the hull itself probably is not weakened with a deep dive, but some critical joint or valve etc may be.

(With regardss to the WTC on 9/11, metal does not soften with stress or pressure. It does soften and weaken with the heat of fire, but that is not an issue here for sub hulls).