In general I agree with Tyronec there.
It is a very common problem of many strategy games that Axis cannot devote any production to ships in general (and the Allies in turn can pratically do the same).
Ultimately some games have sorted it by 'forcing' production in some sectors (read: you have shipyards, you can produce which ships you want but these shipyard works persistently, etc, to just give more production to anyone with full freedom in how to invest it, it will just mean 'more' of what is deemed useful)
Presently I don't touch the navy with a long pole, be either surface or subs.
I hardly tech them as planes (as it should be) minces them and the impact in the game here is quite minimal in the ocean. There is pratically no way Axis raiders, surface or not, can intercept convoys and the like from the USA (troops included - which is something cool of WiF for instance).
As Axis your fleet is pratically redundant.
The Allies will use it, but mostly under the air umbrella of their fighters to shrink to nothingness any Axis port oversea.
But it's very hard to capture the naval game in general in WW2 games. (Then again I am extremely happy with WiF one that barring rare specific situation is solid). But even in WiF, the Battle for Atlantic is often non existant. (Same reason as above, it is better a sub in the Atlantic or an extra INF corp in Russia? The INF!)
But even if BfA would work, then fat chances are that the Soviets will be going rampage in '42 due to a depowered Wermacth.
Prolly the system whole should have been abstracted (as other games do), and submarines are like escorts. To be assigned to convoy routes offensively and then some math is done comparing subs vs escort and quantity of merchant marine used; and some variables that are tech and luck based.