As far as I can find, there is no historical basis for the Black Spot in relation to piracy whatsoever. If you good for it, all you'll get are unsubstantiated sources with a host of reasons that came from who knows where. Beyond that, apparently some plants and fish have diseases/sicknesses called black spot, but I have no clue when those names for those diseases came up.
Pretty much going with Robert Lewis Stevenson invented the device of the Black Spot for Treasure Island. I don't remember there being a curse attached to the black spot until Disney re-purposed it for the second Pirates film. It all seems to be just made up stuff.