Is the core issue of your post that you feel a Submarine is too much of a threat? Because of the pinging/homing torps?
Co-Op gunners used to be dead-on accurate. Every enemy ship was a threat in terms of gunnery, though the basic pathing/behavior made their play predictable and out-playable. The fact that the Submarine is accurate harkens back to the way every ship was accurate... so I'm not quite seeing the issue. Is it more that the Submarine feels "too accurate" compared to the inaccuracy of the other bots?
-
As for how to deal with AI Subs, you just kill them. The AI stays on the surface and the pings give the Sub's location away. Shoot where the ping came from and damage the Sub. They use the same form of AI as the other bots, so they mostly go forward to fight/die like other things.
If you are playing a Sub, it may be hard to land much damage in a higher level environment but they aren't Tech Tree ships that require XP. Their use in Co-Op is for feeling out mechanics in a more straightforward setting or just playing for the sake of fun in a straightforward setting.