I've done this, with 1/600th aircraft and subs.
Didn't bother with search phases, though you could bolt those on.
Ran mine during the "fight back" period, ordered by Adolf, and put a couple of subs on the tabletop, sailing in formation for mutual protection. Gave them uprated flak guns to help. Also, Ju-88C6s for top cover.
Pitted them against rocket firing Mossies, and a couple with those nice big cannons the "tse-tse" variant carried. Good fun.
In real life, the pressure hulls of the subs can be surprisingly resilient, even when surfaced.
Some of the Mossies had to take on the Ju-88s, while the others went in after the subs.
We used Action Stations for the rules.
Good fun!
Sometimes, there would even be a third sub, and a surface escort too, by Sperrbrecher, VP Boats, etc..