Color actually does affect emissivity of heat from an object. The way it is, colors that reflect electromagnetic energy well are also poor at emitting it. Similarly, colors that absorb EM energy well reflect it well. This is why most heatsinks on consumer electronics (like power amplifiers for home use, for example) are painted black.
Don't forget that there is an entire spectrum of EM energy that we cannot see. Underneath the hood of a car, there won't be any ambient light to heat up the supercharger, but by having a dark color to improve emissivity, it can help. However, keep in mind that the thickness of the paint also has an effect on insulating the SC, so too much paint and you've just negated the value of painting the SC.
But considering the temps at which the engine operates, I don't think it really matters all that much what color the SC is.