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> I've always felt the more compelling reason is that a blacklist is never a list of black items.

Why assume it's the items that should be black and not the list itself?

Really, blacklists have nothing to do with the color of lists or the items. It's from the 1400s when "black" was used to mean "censured or disgraced". We see that in phrases like "Black Mark" (as in "a black mark on your record") where at least the mark presumably had a color (“a black cross or other mark made against the name of a person who has incurred censure, penalty, etc.,”).

In that context it makes perfect sense for a blacklist to be a list of things which are being penalized/censured and for an opposite list to be described with the opposite color.