You can add your proficiency to the AC of the ships
If you are using the optional rule from Xanathar's Guide to Everything, you are able to sum your proficiency bonus to the ship's AC if you have proficiency with water vehicles.
Since a ship is composed by multiple components, and all types of ships don't have a single AC value for the entire vessel, you can add your proficiency bonus to its parts.
If there were separate AC values to the components and to the entire vessel, I would argue that you only add the value once – to the entire vessel's AC – but that's not the case.
By cross-referencing the information provided on water vehicles by the Player's Handbook and Ghosts of Saltmarsh, we can confirm that the rule in Xanathar's Guide to Everything is meant to affect the ships published in the adventure.
On the page 157 of Player's Handbook, you will find the table for Waterborne Vehicles. It cites that the vehicles are: Galley, Keelboat, Longship, Rowboal, Sailing ship, Warship. All of this vehicles have stat blocks in the Appendix A of Ghosts of Saltmarsh (starting at page 186).