Only 18 Japanese submarines out of 127 lost in WWII were sunk by Allied subs (16 by US subs, 2 by British.)
http://www.combinedfleet.com/ss.htm
Of those 18, I suspect that the vast majority were caught by surprise on the surface and sunk.
So all that's needed really for SHIV is Japanese submarines that act like the AI ones in GWX - i.e. sailing as surface vessels, and being sunk like surface vessels.
For realism, only torpedoes should be used against a Japanese submarine in SH4 - never the deck gun.