[Greystone]

For what it's worth, I've found that sneaking into an enemy harbor to be the best of the available missions in terms of offering a respite from the doldrums of wandering around looking for something to sink. It provides a chance to get some tense excitement out of the game. At first I was intimidated by the very thought of such a mission, but now look forward to them.
First, make sure your sub is equipped with radar. Get as close as you can to the harbor entrance without being detected and save the game, preferably when it's dark enough to erase all evidence of daylight. Then start heading into the harbor; your radar will let you know who's where in order for you to avoid detection.
When surfaced, your lookouts will inform you of any detected shore bunkers. (I believe they're also detected at periscope depth with the periscope). The consensus on the forums places their range at about 6 nautical miles, so keep out of their range, unless your at periscope depth.
I know it looks like you can't go to periscope depth in such shallow water, but in fact you almost certainly can without scrapping bottom.
You may have a long way to go if you need to be submerged, so keep it at ahead one-third to insure you've got enough juice to get you to the objective & out of there without your batteries going dead. Don't worry, I know it's slow-going, but you've got all night.
If you'd like to continue using diesel & have access to your radar, go for decks awash instead of periscope depth, which are:
Gato: 28', Balao: 28', Gar: 32', Porpoise: 28', Salmon: 31', Narwhal: 30', Tambor: 32', Sargo: 30', S-42: 26', S-18: 26'.
If periscope depth is the only way to go, don't forget to rig for silent running before getting within detection range of any warship.
People here may have other insights or suggestions.
What the hell, give it a try; you've always got that save you made earlier...