Well I have no skills, but I could maybe throw a few ideas at you (I'm an idea guy, it's in my siggy!)

For clear water you just use nebula backgrounds of appropriate tint.
For "cloudy" water you use a full nebula (minus the lightning of course)
All missions would probably use a large ground model.
We have one made by Venom/Nico you can use for testing.
In fact the dome/skybox that was released in same modpack you can remove the background sky image and use a water one...
This is the ground and sky look, (use your imagination) I'm not motivated enough to try it myself, I'm still trying to get the energy to make it the arctic for SG-1 and have the f-302's attacking gliders for a demo pic...
Please forgive the ships in the way, I don't have a pic of just the lanscape...

That sounds like an interesting book, I'll have to check it out sometime.

Anyway I thought subfighter were first mentioned in SEAQUEST? For more info or just ideas on them you can also look up a property called DEEP ANGEL.
I also think they renamed to EMPIRE. Lots of cool concept art on subfighters (most of them can also go into the lower atmosphere as well)...
Good luck with your project!