Changing the water colors won't effect sensors. Just saying they're many other values that effect overall water color and effects in scene.dat file. However, you can change water color in the env.atl file and be OK. As far as I know, the only values in env. files that effect sensors is light values, like sun to sky, but not so much during the day as night.
For instance, I like more moonlight at night with lots of light reflections of the clouds near the moon, why the opposite horizon stays dark. Since light brightens, it will change the color of the water. This is a change you adjust in the Env. file. Plus you can adjust width of reflection, etc....Of course more light at night means better AI visuals, but I think that realistic and prefer it.
Same as above, just opposite of moon.
My advice is to try caustics Improved Stock Env. mod I gave you the link for, that will probably give you what you want.