I second what Paul said. Water or waves are just an effect and have no physical properties except being a hard surface (for landing and crash detection). If you look closely at the shoreline you even will notice that the 3d waves continue a tiny bit on the land surface, so I suppose the tesselated land and the moving water surface are rendered as part of the same 3d model with limited special properties to each part.
Static models of ships don't bob on the water surface, and it appears that simobjects that do bob do so in a disconnected way, it's just an algorithm that lets them pitch and roll a bit, hence this is not a model that is connected to the properties of the moving water surface.
I also observed that "water" is not excluded in 3d models that are "hollow" and have open space beyond the waterline. The waterlevel just cuts through the model and appears in the ship wherever it can be visible. That's the same on land, except that we have tricks here that can be employed to sculpt the land surface and make room for pits or submerged hollow cavities.
However, knowing that P3D is a large beta stage project, I'm confident that things like that will be addressed sooner or later. I also don't worry about the math and impact on the sim - today's systems are extremely fast with math calculations and there are even frameworks like the PhysX engine that explicitly deal with the simulation of natural environments, like water (every, even older Nvidia GFX cards can employ that).
It is also interesting to have a look at other Sims or FP shooters, most of what we want or ask for has been done before (e.g. Silent Hunter or the latest FP games).
Cheers,
Mark