Im fairly new to this excellent engine, but i got a fairly decent idea of what you mean and how to possibly do it.
1)
You can do this, but, you could also make it deep enough (as it was in waterworld when you see kevin diving down with the famale, its fairly deep), so if it is that deep, its out side of the render view distance, so it isnt rendered while over water (use underwater fog to mask those things).
But i would probalby (based on depht) just let it all render, and use auto LOD on the models, you cant see the models clearly if the water is scattering anyways (in shallow water).
2)
You can make your own class to handle such things as handles and so on, i belive there is samples on how to do this.
I would probably add those handles ect as seperate models onto the main ship.
To make it walkable on the ship, i belive you need to create a physx hull / plane on the surface you wish players to collide with, this is done inside the model editor (Phys) i have issues with models getting stuck and such, so might take a bit of work.
Hope it gave some ideas, if not (or if im wrong) im sure Esenthel will come correct me