It's looking really good.
The main hull looks great. But because it's so well textured it makes the fin in back stand out a little more to me. Whether it should be overall more midtone? Or add some shadow to the bottom of each plank to give it depth? Not sure exactly. It just seems like it's a little brighter than the main hull. But the wood texturing and rivets look great to me.
I like the shading you have on the 3 windows at the side, but I think you could take it a step further to show the curvature of the windows with the highlights. I did a rough attempt that hopefully gets the idea across.
As for the animation, I know it's not strictly pixel art, but I like the water affect on the plants in the animation you have. Looks really natural. I'm making an underwater game myself, and it's tempting to throw filters on things and it's hard to balance what looks natural with the pixel art and what seems like a cheap affect to give movement to still pixel art.
The godrays are more up to personal preference, but I had good luck using a solid transparent color and having them overlap. They don't look as "real", but they seem to blend better with the pixel art. You might also move them behind the sub. When they are in front and the lighting on the sub doesn't account for the depth and "form" of the sub it's easier to tell it's just a layer in front of the sub. It may also make the sub contrast more with the background? Then again it may compete more with the background.
Looks great overall though.
Side note: the menu options look nice. I always struggle with UI stuff and it looks really natural here.