I am only using IuB and SH3 Commander (which doesnt add ships) only. It seems that not every port will be populated with ships although i think you have a better chance to bag some at actual ports than psuedo ones. What i mean by that is zoom in on the port your thinking about entering, If you see a harbor area you will have a better chance of spotting ships than at the ones when you zoom in on would only have the red dot and not an actual "built-up" harbor.
I went to Hartlepool in 11-1939 as suggested and found and sunk 2 C2 Cargo ships a coastal merchant, 1 Flower Corvette and a V & W Destroyer. There was also a small coastal vessel which i let be and a 2nd Flower Corvette that was inside the netted area and was obstruced behind a light house so i was unable to nick it with a couple of torp. Even moving back to 3000M and surfacing to fire some shells from the deck gun failed to get a reaction other than it continuing to ping me.
Hope this helps, good hunting