From a theoretical heat transfer standpoint, black will radiate more heat than the natural aluminum finish. Most of the heat transfer from the intercooler, however, is from conduction directly from contact with the air passing through it. In that case, the paint could act as an insulating layer. My point - black and natural aluminum both have their advantages.
Having said that, the late 2nd generations like my 2002 came from the factory with the intercoolers unpainted (save a buck anywhere you can, I guess. )
Rusty