I've struggled with different techniques for making "water," and I have yet to come up with a real solution to the problem. For relatively calm seas I've had the most luck (so far) with a piece of poplar (Lowe's stores carry it), carved into "ripples" with a shallow woodcarving gouge. Then I prime the wood with artist's gesso (prime both sides of the board; otherwise it will warp). I find that artist's acrylics are best for the finish coats of blue, green, grey, or whatever. That kind of paint seems to have an inherent depth and gloss that paints formulated for models don't. A couple coats of artist's high gloss acrylic varnish finishes things off.
I've generally avoided trying to depict ships in motion - for precisely the reasons you've indicated. Another consideration: to my eye, at least, freezing motion in a three-dimensional model never quite works. Maybe the problem is psychological, and it may be unique to my perverse personality, but I'm never really convinced by a ship or airplane or tank model that's supposed to be in motion. (A
photograph
of such a model doesn't bother me. Like I said, maybe I'm just nuts.)
Anyway, the nearest I've come to an acceptable bow wave was made from Milliput. If you aren't familiar with that substance you're in for a treat. It's a two-part epoxy-based putty that hardens in three or four hours and can be formed into just about any shape. You're going in the right direction by studying photos of the real thing. Different ships, different bow waves and wake patterns.
I don't think I've helped much, but it's a fun topic.
Youth, talent, hard work, and enthusiasm are no match for old age and treachery.