Japanese DD captains usually followed the torpedo tracks, which is usually why you want to get in as close as possible before you fire.
1.) I believe they can
3.) it depends on the plane, and your location. Close to japan, you will see a lot more air traffic IIRC
4.) depends on the harbor methinks, since American sub commanders would prefer not to risk themselves by bottoming out in a shallow harbor, they would hang out outside them, using the slow torpedo setting. but that's not the point
to answer your question, I think large naval bases have a change in traffic, but typically I think it remains a constant for some of the smaller harbors
5.) no, definitely not, one such torpedo destroyed Dick O'Kane's
Tang, and she went straight for bottom.
6.) another why American sub skippers stayed out of harbors. your best bet is to hang behind it and see if you can snap your shots from there, and If you can't, there is probably an entrance somewhere