I encountered the same "problem" in the later adventures, but thought most of it was due to the fact that Pathfinder tends to escalate in terms of player power compared to 3.5.
The enemies in adventure 11 are deliberately weak because there is no way a party could rest inside the Tempest. That being said, I still found them too harmless for a 19-20th level group, especially the final fight. What worked well for me regarding Pilus and Onamdammin was to take their theme (Pilus' spells and defensives, Onamdammin's leader archetype, the guards' martial prowess, the monk's hit-and-run shenanigans) and buff them massively.
If you can get your hands on the 4e versions, you could take their respective powers as inspiration and give them to these guys. Open Palm Strike and Lightning Palm Strike were both fitting additions. Oh and you can also triple Pilus' HP. He'd die in one or two strikes otherwise.