The deep pour types of products are designed for uses typical in model railroads. Streems where the streambed is visible, or stuff like logs on the bank go down in the water.
It's not really good for ship models for the reason you give, plus it has no real advantage over a surface focused model.
My usual method is to select a board for a base and make the top surface quite smooth. Paint it a base color that matches the color of the ocean where your ship is sailing.
Ocean color is largely a reflection of the color of the sky above. But for modeling purposes there's also a need to have the model contrast with the water.
For the water I stay away from blue, I like black or dark gray.
Acrylic gel medium is stuff like vaseline in consistency, that comes in a jar. it's easy to find it at Michael's and Aaron's. It's art use is to overcoat paintings to give them a texture that makes flat painting art look like oil paint with heavy brush marks.
For your model, if you have a separate hull bottom, or can make a shape 1/4" thick or so, put it on the model and apply the gel around it. Your coat is maybe 1/8" thick. It takes a couple of layers, and waves can be teased up as you go. It starts white but dries clear.
You can add acrylic paint to the gel. Add white for your final wave coats.
One suggestion on waves and wakes. Don't make it up. There are plenty of aerial photos of ships from which the right waves and wake for various hull types can be discerned, or for ancients, copy something similar.
Acrylic varnish comes in flat and gloss. You can decide on the finish you like.
Some people use silicone sealant, I don't like it as it smells and is hard to move around with a paint brush.
I hope that's a little helpful.
Bill