Hmmm, now your are trying my memory. I know that the ship does not adjust for Puerto Vallarta time and stays on ship's time. On one cruise, we had dinner in downtown Puerto Vallarta and a couple we were dining with freaked out when they thought they had missed the ship (Puerto Vallarta time) and scrambled to make it back.
The state of Jalisco is one hour ahead of the state of Nayarit (just a few miles north) so I don't believe that any cruise line adjusts to the hour time loss when going to Puerto Vallarta.
However, they do adjust to the hour loss when you visit Cabo and Mazatlan. So I guess the answer is they only adjust to half of it. VBG.
In fact, my family and I just spent a week in Punta Mita (Nayarit) looking at property along the northern Puerto Vallarta coast and which time we we going to meet the realtor, was a huge consideration.