As I recall, one idea HiTech was toying with was having a wolf pack (sub spawn point) that would be moved just like the CV. You'd get it into position or have it patrol. Then, a player could spawn a sub from that location like the CV spawns a PT or LTV. I would imagine it would be cool if ports could spawn them as well, again just like PT boats are spawned. One good use of a sub is to pop up to the surface and begin shelling bases and towns (typically carried a deck gun in the 3-in range). A plane might up to try and sink them, but the sub could just dive and go deep (assuming they have enough water under their keel) so they can't be spotted. Recall too that on the surface a sub could make upwards of 16 knots (~ 8 to 10 knots submerged, but that would drain the batteries pretty fast). So, while they'll never run down a CV group, they can move to intercept a surface group. They'd present a unique challenge to defend against. While submerged, I'd let them get to within say two thousand yards before the CV begins to flash; when the sub is surfaced, I'd say a CV should start flashing when the sub is within ~1.5 to 2.0 miles.
Of course, adding subs is a huge investment in time for HTC, as so many pieces have to come together to make them a viable game option.