Great mod, Rongel!
As of the realism of firing at a submerged submarine, to my knowledge most of the secondary naval guns had special anti-submarine shells, AFAIK they were diving shells - special shells with blunt nose so you shot it into the water and it did not bounce of the water but dived and continued for some distance submerged hopefuly meeting the submarine. Moreover you read in reports of real ASW actions that planes often strafed the spot where the submarine had submerged with their guns, I recon that it is modelled in the AI logic by developers, that is why, I recon, the ships continue to shoot at the last known spot for some time with your mod as well since they use plane's script, I recon that is realistic as well - why would a ship not want to shell the last known spot knowing that the sub is relatively slow to escape? Imagining myself as a DD captain I think I would still fire guns at last know spot for a couple of minutes even if I did not see the periscope any longer and even if I did not have ASW shells, at least there is some hope that a shell would strike something fragile or the sub would be damaged by the HE-shell explosion, even if the shells did not strike they at least would force the sub to be frightened and stay submerged so negating a possibility for the sub to attack me or the convoy - you see enemy, you shoot.
The only unrealistic thing I see is the fact that they continue for far too long when you submerge while it should be no more than a minute or two in reality.
If only we could get of the friendly-fire issue... but it is not this mod's issue since if planes do not check for friendly-fire condition they can strafe a friendly DD on a DC run. That means that it is a stock AI error.