Automated targeting doesn't change anything about armor classes because you can already shoot at them manually. Either the targeting should be automated or the water penetration of the projectiles removed. Do you mean that the removal of water penetration would bring the sub armor class back and would therefore be bad?
For most of its existence, ZK had an armor class named "sub" that received 5% damage from all non-antisub weapons. This was removed because changing Seawolf preferred depth allowed it to avoid most of the aoe anyway.
Mistral becoming a problem is most easily fixed by reverting this change, second easiest solved by a reduction in Mistral AoE, third easiest by making Seawolf submerge deeper, and is very unlikely to be solved by declaring Mistral to have essentially the old Crusader Depth Charge sidearm, as per the OP.
in that case, automated targeting would be the preferred solution.