It is true that the actual number of CV’s and other capital ships sunk during WWII by submersibles is small compared losses to aircraft (not counting escorts, which actually suffered quite significant losses). However, the threat of submarine attacks made a huge impact on the operational doctrine for CV and surface battle groups. They were almost never risked in littoral waters, for instance, and seldom operated at night for fear of submarines seeing the deck lighting. It also forced surface combatants to zig-zag constantly, except when launching and recovering aircraft, thereby slowing their strategic speed and mobility.
The fact is, submarines in AH would radically impact carrier operations in the game. Remember that in AH, CVBGs usually steam in close to shore, both to shorten flight times and to allow shore bombardment and amphibious operations. Submarines would have an easy time against an enemy CV fleet that is trolling back and forth off an enemy base (ducks in a barrel, so to speak). The aircraft carrier’s greatest real world asset is its strategic mobility, something neither appreciated nor even applicable in a make-believe world where targets magically rebuilt after 15 to 30 minutes. What it would change in AH is how long a CV could hope to survive once it was committed to assaulting a base. The moment it is spotted off shore, enemy subs would begin to converge like teenagers at a Golden Corral buffet. Indeed, subs would spell the end of amphibious ops in AH in the absence of a massive collaborative effort by players (and how likely is that?).
Another problem for CVBGs is that they currently spawn in a predictable location. Upon spawning, they would then have to run a gauntlet of waiting subs before reaching the relative safety of the open oceans.
In fact, a number of things in AH would have to change to avoid completely unbalancing the game by adding subs. In addition to the obvious need to develop player-controlled ASW assets, sensors, and weapons, fleet spawning would have to be made much more random. Likewise, players would have to maintain continuous control of the helm (and given the ability to take direct control of both helm and speed, versus the current waypoint navigation system) while in close proximity to enemy subs. Finally, specialized fleets would need to become standard in the MAs. There would need to be at least two types of TGs, the CVBG and the AABG, or Amphibious Assault Battle Group. The former would not have either PTs or LVTs enabled, while the latter would of course have not aircraft, since they would not have a CV in attendance. Alternately, you could replace the fleet CV in the AABG with a smaller, slower CVE (escort carrier). The CVE would only have lighter aircraft available, such as the FM2, Seafire, A6M, Dauntless, Kate, and Val. The CVE’s slower speed and shorter flight decks would make operating a heavy fighter nearly impossible anyway.
So you see, it doesn’t matter how many CVs were sunk by subs in real life. It only matters what affect they would have in the artificial environment of AH. I say, “Bring ‘em on!”