I've seen this. Genetic predisposition to a melanoma is what I've heard. Try breeding it out, or starting with different stock. Fairly common in AUS as everyone breeds everything and imo doesn't cull enough.

If I'm understanding correctly, the black marks are in a similar pattern on each affected fish, do not protrude from or break the skin, and do not appear to affect fish health at least in the short term?  This would not seem like an external parasitic or bacterial infection; it sounds like something is causing the fish to mess with its color cells. 

Melanoma is certainly a possibility, but I would look for  possible sources of stress as well.  I've had customers trade in angelfish with similar markings, and we believe it results from long term stress from crowding.

Since you mentioned " a lot of cyanobacteria", I wouldn't rule out the toxins that can accumulate in those tanks.