The word "Color" in the name does indeed refer to color film. In the case of Yashinon, it does not necessarily mean it is "optimized" for color film, simply that it is capable of being used with color film. The lens is also fully capable of producing black and white photographs as well. At the time, in the 1960's and early 1970's, Yashica cameras were more widely used for black and white photography, so explicitly calling out viable color film compatibility was kind of a big deal.
It wasn't until the 1970's that color film really came into common use, and COLOR-Yashinon lenses started appearing before that time. It seems one of the more popular Yashinon lenses was the COLOR-Yashinon DX 1:1.7 f=45mm lens, commonly paired with the 1973 Yashica Electro 35 GSN.
I don't have a lot of information at hand for the Color-Skopar, and there seem to be "classic" as well as modern lenses that bear that name but are not related to one another outside of the reuse of the name in a modern Leica lens design. I gather, however, that the classic versions came out of the 1950's (an even earlier era for color consumer film), and I assume the purpose of the word Color was the same as in Yashinon lenses.