Go here
http://www.wargamer.com/articles/aces_high_interview_main.asp to read what Dale said about subs. He describes a bit how they would likely work. Yes, it would be an ambitious project, but one that he wants to do at some point. From what he told me, it sounds like there would be a fleet-like element -- call it a "wolfpack" that would move on the map like the current task force (albeit a bit slower). Players could set way points to move the wolfpack into position, then players would spawn a uboat from that location. At that point, you would make attacks on your targets.
In addition to torpedos, subs back then carried deck guns (usually 3-inch, but one French sub actually had twin 8-inch guns), machine guns, and mines, so they would not necessarily be limited in how they could be used. While slow underwater, they were considerably faster on the surface. Indeed, many night attacks were carried out surfaced. So, subs could be used to set up minefields in chock-points or to discourage bringing fleets close in shore. Remember too the rather unhistorical employment of fleets in AH, cruising back and forth off an enemy base. In this case, subs could literally surround the enemy surface fleet and fire salvos as the crossed back and forth (ducks in a shooting gallery). Sure, you'd have to be lucky to get carry out a successful intercept and attack on the open oceans, but our AH fleets spend little time in that element. Instead, they are used in litoral waters, where slow "pig boats" (US term for diesel-electric subs) are most effective.
The biggest challenge for HTC would be surface ASW, since that requires direct player control of a DE or DD, implementation of sonar, hyrdophones, and myriad of other details in modeling the surface and subsurface environment. Nonetheless, it would be a great addition to the game.