Let me point out a few things they will need to deal with if subs are bought in:
Running aground - While underwater that would be just giggles of fun
You are in a sub and you get hit by a Yamato's 18 inch shell. It would pass through yet you just got a huge hole in your hull. You need to dive. ummm.... can we say hello bottom?
How many subs were equipped with guns? Guns that can actually do damage to something like a Cruiser or BB?
Get hit in the front or rear with an high explosive shell and BOOM. You got magged.
Remember depth charges only needed to get within 30 feet to crack the hull of a sub. Think what an explosive shell from a North Carolina or just a low level cruiser would do to it. That shell would go boom AND from the force of the impact alone tear a huge hole in the hull.
Remember the torps in American subs had a horrible fail rate early on? Now would that be fun if they put that mechanic in? I shoot a ship, I see the torp hit only to be told the torp was a dud. Lovely.
I'm playing a battleship. Out of nowhere torps hit me and I'm flooding. Now this is bad enough with DDs but now I have to deal with subs too? Joy.
Ramming a sub. A DD could split one like a grape.
To render ONE ship in the game takes like 6 months of work from a developer. Now how many ships would need to be touched to add subs and correct balancing?
You are underwater - if your sub is not showing it's periscope you have NO idea where anyone is.
Radio communications in subs do NOT work underwater. So....again - you have no idea where anyone is.
I could see team killing of subs being a real problem seeing how many people hate them. They would hate them worse than SPGs in WoT and in that game they get lots of grief.
There are loads more things to point out....