Fact is that USA sub commanders would not engage armed Jap merchant ships. The Japs were very good gunners generally and, with a poor/non-existant convoy system, merchants did expect to defend themselves. What's more, a single hit from any decent gun (3" or greater) had a very real chance of leaving the sub crippled.
In other words, you shouldn't be exchanging gunfire with ANY Jap ship, be it Navy or merchant.
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