That is a PtV question and you should make sure with the designers of PtV, But the PtV rules follow the regular rules except as specified.
I think the answer is yes, because there is no requirement that the fighters can make any difference in the battle they scramble to (page 16, Europe manual). If those carriers are sunk, the fighters have a chance to move 1 space to friendly land or an undamaged allied carrier. (page 16)
However, even though the rules have no stated requirement that the fighters have to make a difference (that is, can’t be scrambled against sub only when you have no destroyer), Krieghund sometimes surprises me on questions like this. I think I’m a 90%+ accurate answer but if you want 100% you have to go to the Q&A thread. Even though the regular rules don’t provide for carrier scrambles, the same question applies. I think the heart of your question is whether planes can scramble to defend
against subs where the planes will make no difference, and that question is relevant to the regular game as well.
https://www.axisandallies.org/forums/topic/18412/global-2nd-edition-q-a-aag40-2
So you won’t need PtV guys I don’t think. If you don’t want my “quite sure” answer, go here and ask Krieghund if you can scramble to an attack by subs only where you have no defending destroyers.