It would be good if destroyers were paired with enemy subs for the purpose of negating the sub's special abilities. As it is now, one destroyer can negate an unlimited number of subs. Also, if subs could target ships of choice that would be good, similar to how strategic bombing is handled.
I've thought about better sub rules for a while, and this post made me realize that there is an alternate way!
Its possible to make subs strategic bombers, but they would need to be air units. Its possible to ban them from entering land territories, and set carrierCost=0. This would mean that it can fly over enemy units of course, so if you made destroyers anti-air that only affects subs this would also allow to make the relationship work on a 1 to 1 ratio! Destroyers will NOT be able to stop subs from moving through totally, however they can shoot at subs that are passing by, and subs wouldn't be able to submerge.