I've never encountered anything interesting in harbors, except late in the war I went into Valletta and discovered the interred Italian naval capital ships and sank them.
I'm sure other players have figured out what harbors to go into when to discover nice targets. But every other time I've gone into a harbor there are just a few ships and nothing very interesting.
Of course you always run the risk of mines and nets. With external camera or raising your periscope a little bit you can (unrealistically) avoid mines and nets.
Just last night I went into Scapa Flow (December 1939) with 100% realism and did not hit any mines or nets.
Of course there are usually a couple of escorts that come to investigate when things starte exploding, but the escort AI goes all wonky.
For example, I went into Scapa, and nailed 3 ships, and the escorts came charging in from the bay. I simply pulled my sub alongside a tanker at pier and the escorts could not get near enough to me to do anything - their AI made them slowly putter about at near-zero speed, hovering near me, and I popped them both with magnetic torpedoes.
While I was parked next to the tanker I was imagining crew men running around up top getting big chains ready to grapple my sub with.
Steve