Let me clarify my reasoning on point number 2:
Submarines defend at a zero because they are not firing back, they are battening the hatches, flooding the ballast tanks and adjusting the dive planes hoping to get below depth charge depth before being sunk. (Which is silly, I guess you should say destroyed not sunk, since they sink on purpose…)
Meanwhile, they attack at three because they quietly slip into range, hide in the waves, line up their shot just right and fire. Since there is resistance to giving them called shot abilities (where they tell us who they aim for before firing, like Kaitens and Kamikazees did in AARe) I figure this is a solution that would work.
Also, it should be mentioned that I am assuming Super Submarines has been changed to Super Destroyers which would increase Destroyer Attack Power = to Submarine Power.
Submarines do not defend with a surface fleet, they travel solo usually way out ahead as scouts or raiding enemy shipping. Treat them like transports if they are detected and defenseless.