Holy Water/DJH lists treasure stealers/swappers as direct affects that it protects against. I take it to mean that any other treasures on the same ship would be protected as well, or do the Water/Heart only protect themselves from being swapped or stolen?
Treasure stealers and swappers have to target the ship in order to get at any treasure being carried by it, so Holy Water/DJH will block them.
Kharmic Idol, Pirata Codex, and Jailhouse Dog bypass the protection because they specifically go after Water/Heart itself, without going through the ship or its crew first. They don’t even care if it’s on a ship at all.