The ports are too easy actually.
I don't know of any deep water ports. Mostly it is shallow. You can be at periscope depth but usually have less than 10 feet under the keel.
Most of them just have some subchasers and gun boats. The problem is that they will not come after you. They will shoot at you from the dock though. These ports will have some merchants docked. Occasionally a destroyer. For instance I went into Saigon and Vau Tung (only because I have actually been there IRL) and there is an active destroyer.
On the main island of Japan there are warships in some of those well protected ports (Kobe comes to mind). There are active destroyers in some of these but if you get past them it is easy picking and the warships don't fight back. I have not gone up Tokyo Bay. I considered it but was met with 4 aggressive destroyers at the entrance.
__________________

USS Growler (SS 215)
February 7, 1943
|