Ok, I always feel like I'm cheating when I do this, but I do raid harbors in my S-Boat if I can't find targets out on the open ocean. What I (former artilleryman) do is watch the DD and observe his patrol pattern for a while. Normally in Honiara, the DD runs a triangle pattern with the point of the triangle facing the harbor. This means he's doing a long , straight run paralell to the docks, about 2000 to 3000 yards out. Simply put, I creep up to about 6000 yards of his path, wait for him to turn his side to me, and let him have it with long range deck gun fire.
It always works. At the long end of his pattern, he's too far away for the docked escorts for them to see you and assist, and if you can start hitting him at 6000 yards, you'll sink him before he can hit you back. Easy-peasy
Sure it feels like cheating, and I only use it when I need the tons, but once the patrolling DD is sunk, you can sink as many docked ships as you want. Stationary ships will not start moving just because they know you're in the area. They just sit there and wait to die.
P.S. If you really want a "rickety" old S-Boat, try WEBSTER's "S-Class mod for v1.4 & 1.5." 10 knots flank speed, 5000nm range @ 6knots, 200ft crush depth, and only 25% armor and hitpoints.