Ah, but we did. We very specifically authorized the USN to engage in "unrestricted submarine warfare". As such, every Maru in the Pacific was fair game. And that is why public dispatches in WW II did not identify submarine capatains and crewmen by name (at least, I believe that's the case).
One target sunk by a US submarine, for example, was a "prison ship" which was transporting POWs from The Phillipines to Japan. There are several such cases, reported here.
There is simply no practical way for a submarine commander to determine whether a merchant freighter is carrying military personnel and/or materiel. But, in a war zone, an enemy-flagged vessel is presumed to do so.
As I recall, since Japan was not a signatory to the Geneva Convention, and they demonstrated by the way they were fighting the war, that lighting the insignia on the ship would only invite the Japanese to attack it and ships around it, so it was deemed safer to stay in a darkened ship condition.
And you are correct. We did engage in unrestricted submarine warfare.