Of course it's a simple matter of solving the equations given by
Airy wave theory 
Wikipedia is pretty good at ocean wave models. Well, better than I am at maths.
There's some more comprehensible but a tad less scientific stuff
here (I think this reference is an approximation). This second reference says that in deep water waves should be "felt" down to half a wavelength, it gives an example of an ocean wave with a wavelength of 48m being detectable down to 24m. The amplitude obviously scales with the surface wave height and the motion of the boat should also get slower with depth as the short wavelength waves get filtered out. Wikipedia recons ocean wind waves can have wavelengths of 60-150m so therefore would be detectable at 30-75m.
i assume a sonar operator could hear rain and also tell if there were breaking waves - anybody got some hard info? It seems to me the SH3 GUI's which display the surface weather at all times are closest to reality.
Pity that the SH3 weather model is so poor. i think it's because the campaign mode was an afterthought late in the development.