I think submarines would be a great idea. So many other games have incorporated the "Now you see me, now you don't" angle such as STO (Star Trek Online) with the cloak ability, Halo with the active camo & Battle Pirates (on Facebook) also having submersible craft. The mechanics and idea is out there so why not make it part of WoWS? I agree that the ability should have a cooldown after resurfacing but not whilst submerged.
I appreciate that this would be a hard thing to make fair so why not make the submarines only available in the higher tiers for example? This way, the player is up against ships that can destroy the sub in a couple of volleys. Something else could be to reduce the turn rate of the sub which would both solve the fairness problem.
As for surface weapons, I don't believe the original design of the submarine should be "tampered" with too much so I think that the sub should have 3 or 4 torpedo turrets that can be fired whilst the sub is on the surface with a couple facing forwards and a couple facing backwards - solving the surface weapons issue.
To make sure it stays as fair as possible, maybe it could be designed so that you can buy a sonar pod or something similar which can be placed on any ship to allow it to spot submerged subs from a given distance. Maybe some sort of underwater-defence system could be developed so that the subs could be seen and a rapid-firing mini-cannon would be able to fire at submerged subs (not doing much average damage - to keep it fair) in one instrument.
Just some ideas to keep devs occupied.
