Alright lets answer some q's.
First about the water surface. It can be done in several ways (I've tried a bunch of em on this project).
One option is to use the fluid effects and the ocean (try using one of the presets and modifying its parameters, to give you a starting point). This has the advantage of being quick to set up and get looking alright, and has some serious options to get it look awesome. The main drawback with it is that it requires Unlimited and that it is very very slow to render (the more fine waves, the slower). It has some other advantages as to an pretty cool shader with highlight glows and stuff.
The other main option is to do it with nurbs planes and animated displacement maps (for this kind of water it works well). You will have to put alot of effort in the shader and also more work in post (with glows and things). The advantage is that it is alot faster to render and can be made to look as good. It is no simulation but whatever looks good is good.
The fog effect is a simple environment fog in Maya, looks alright. The seabed uses some paint-fx seaweed and plants. They actually move, but so slowly that they look static in the animation.
About rendertime. It is a 4 stage process, first render out the hardware particles in Maya (a few minutes). Then batchrender the entire sw-render part with depthmap channel (roughly 10h). Then composite the two (I did it in an old version of shake for NT, but After Effects or whatever works). I also did color-correction and some various glows and DoF in post. The result is rendered to uncompressed tga's (a few minutes) and then loaded into VirtualDub to compress it into a Divx .avi (done in realtime). Rendertime explodes when using fluid effects, but is reasonable with disp. mapped water. Times are with 640*360 resolution, a 1280*1024 would probably take roughly 4 times as long.
Sorry if I rambled on, but I hope you got your answers.