I've raided the harbor at Rabaul numerous times, though I don't recall ever attempting it in an S-Boat. I did go in with a Porpoise Class though. The problem with Rabaul is it's isolation. You never know what you'll find until you're actually in there. Sometimes, there is an additional patrol boat inside the harbor, but I guess that depends on the mod you're running, if you're running any.
Usually, I enter and exit from the shallow inlet to the SE. There's always a DD, a Mine sweeper or subchaser patrolling the outer perimeter. I always take this patrol craft out as stealthily and expeditiously as I can by sneaking up and torpedoing from a high speed range. You have to lead the target since they usually speed up just prior to impact, so aim slightly ahead of center. Once that boat has been dispatched, you have to go in at just below "decks awash" depth (
or just deep enough for battery power) just prior to hitting the harbor's shallows and WATCH OUT for the shore guns. You may not always see them, but they're there!
You may also run into a Sampan or Fishing Boat once inside. Ignore them, unless they get too close or are blocking your approach. You won't be able to see everything that's in there until you clear the bend on the right. Since the ships are docked, you can use a long range attack to avoid getting any nearer to shore installations. Usually, I find the harbor replete with fat juicy targets. On a couple of occasions, I wasted a lot of time and effort to find a few low tonnage targets.
Good Luck sir. In an S-Boat no less, you got big 'uns.
Oh yeah, you always run the risk of getting caught in the middle of incoming/outgoing traffic. I once narrowly missed being mauled by five (5) DDs that were on their way out. It was all a matter of happenstance timing that saved me.