Yes you are actually placing the wax on the clear coat - not on the "black" or the base coat. However, certain waxes may look better on certain colors. The wax doesn't have to actually touch the pigmented paint to provide this effect.
This is mostly subjective, but there may be some consistencies in the theory. Some waxes may have pigments in them (CGs Black, BF Monton Wax, Dodos PH/BV), the may slightly darken or alter the look.
There is no doubt in my mind "wax" can change the look of paint. Although it's subtle - it does exist. So, it seems to make sense to me that certain dark waxes can darken or alter the look of how dark paint appears - or any other color paint for that matter.
Then again, there are waxes that seem to look good in every color. See recommendations above.
I don't think it matters if your working on clear coat or not when choosing a wax. If you want to choose a wax formulated for dark colors - go for it.
Sent from my iPhone using Tapatalk