You may well be right. Over the years I've made so many mods and tweaks so I'm not always sure of any given file's original source.
I just looked at my MAW install and the copies I have of what I thought were the original water animation files I have archived are 256 x 256, colored blue, and the animation runs north to south. (Makes me wonder where these actually came from if they're not the original MAW files...)
The ones provided with the shader pack (evidently borrowed from MAW) are 512 x 512, are in shades of grey, and run East to West.
I do remember in the early work with AnKor that the color of the wave animation files was determined to be irrelevant because they were only being used for the bump mapping and sea foam threshold, so we went with shades of grey only.
However, the color of cfs3h2o.dds did have an effect when combined with panoramic_cubic_test.dds that was used for the surface reflections at the time.
More recently the surface reflection colors are taken directly from the environment dynamically rather than using the static image so the panoramic file no longer plays a role in this, but the underlying color of the water in cfs3h2o still does as seen in Gecko's work.