How about simply putting in a hell of a lot more mines?
Most WW2 ports were protected by defensive minefields, even those of neutral powers.
The fields mostly had a single gap or two which was swept daily and also protected by antisub measures like nets which were lowered only for entering or exiting vessels.
I sofar have failed to run into a single mine in SH4, but I am not a harbor sneaker anyway.
When looking at the minefield file in SH4, you see that only large scale defensive minefields are there, as well as some minefields blocking straits like the Sunda or Tsugaru strait.
No defensive minefields close to japanese (or american) ports at all. Or are they stored in a different file.
Main problem would be to prevent the patrolling japanese warships from blundering into their own mines. On the other hand, with mines in place one could safely remove those escorts anyway.
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