Ship hydrodynamics studies ship motions. But the actual water waves in nature are typically nonliear. Since they are not ideal sinusoidal waves, there are no distinct crests and troughs. How can you readily tell where are cressts and where are troughs? There are also other complicated phenomena involved such as wave breaking. Only in water tanks in labs you can create regular waves using wave makers, but in this case only ship models can fit in your water tank, not the actual ship hulls any more.