The first airline I flew for had colored manuals. I can't remember the actual details but I seem to remember the Ops manual had a blue cover, the Vol 1 was a green cover, the SEP/Emergency manual had a red cover, not unnaturally. I seem to remember a brown one somewhere!
In my engineering training days of Technical drawing, we used nice colored pencils to enhance the look of the work. I'm sure that if you have a drawing of several systems on one page then color is indeed a great benefit.