Ok made it! ..And that should be the final version! :)
I've fixed the doubling issue and I've imposed a saturation level for colors... now the game should look well I suppose (make me know if you have any suggestion).
There where two vertex shaders for the water, one for the superior surface and the other that simulated the seabed. At first I've tried to fix the superior surface thinking the doubling was a plane's shadow issue but I've not been getting any good result.. then I noticed that decreasing convercence caused the doubling halo to disappear... so at the end I've removed the doubling issue by modifying the old water shader adding a 'slt' instruction, so that it can change convercence value's sign when it is less than the actual vertex depth value.
I attach the complete shaderoverride folder, an image of the final version and an image with the game in its original state (should be good for the wiki..)
@Helix: Great job for skyrim fixes! It's a great game and it deserves this treatment! :)
Edit: I've also edited some pixel shaders adding some transparency to the hud and pilots' names becouse I think it allows to see better.