Even more, the color black itself has many different connotations, and not all are negative. It is for example a color of formal prestige (black belt, black ribbon). It is high-contrast (the situation is black and white). It is the color of things which don't emit light (black body radiation, black hole). It is also the color of many bronze statues, and also of ebony - both often used to depict saints and Jesus himself all in black since medieval times.
Humans are perfectly capable of keeping context in mind, and connotations from one context don't actually bleed into other contexts all that much.
The missing representation of black people in European and American art is a different problem, and it is a real problem that won't be addressed by replacing black box with opaque box.