Hard to tell from the pic but are the very small and uniform or are they irregular in shape? If the are uniform and very small it could be Black Ich. Otherwise said:
i think it is the latter
what is hyper-melanism? and thanks
Are the clowns hosting in some coral as opposed to an anemone? Clowns will get black marks from hosting in some of the LPS. It can clear up as they eventually become more tolerant of their host.