Without torpedoes a PT boat is kinda useless, I guess these are only for decoration. Probable trouble is the SH3 legacy, Germans didn't have much in the way of a surface fleet so there weren't many surface battles. Apparently this game is designed to have the player sub only fire torpedoes, so that kills that idea.
"Perhaps too close?"
No, it's not in the waypoints, it's the AI (Artificial Idiots) that alter course toward the target, speed up to 44 knots, then slow down and stop within 100 yards waiting to be turned into toothpicks. I've seen most of them make what looks like perfect firing runs but they just never launch a torpedo. Maybe they left them ashore and have all four tubes stuffed full of beer.