Yes, you should definitely make battleships weaker yet against submarines. To balance things out destroyers could be even stronger against submarines. Battleship captains feared submarines while submarine commanders feared and ran away from destroyers. There is only one case in history where a battleship sank a sub and it was by ramming. It is just weird to see a battleship sink a submarine.
Cruisers were also useless against submarines during the first half of the 20th century. After WWII with missiles and smart torpedoes cruisers gained ASW capability. It would be cool if it could be programmed to so the relationship changes with upgrades. However, battleships even today remain susceptible to subs because of their older vintage machinery causes them to have an extremely loud acoustic signature (10 times comparably sized CV) making them easy targets for submarines.
As far as costs both subs and DDs cost a much smaller fraction of what a BB does.
I realize that this is more of an abstract game and historical accuracy is not the ultimate goal, but I think making subs able to take down capital ships while being easy prey for DDs and perhaps some aircraft would make the strategy and tactics much more interesting.