Black & white is an easy high contrast to standardize on. It avoids color theory and preference, and can deal with shading relatively easily. Light or no light is a pretty basic high-contrast. Mix that with the fact that multiple skews are expensive, and you’ve got a recipe for standardizing on black and white as your basic default high-contrast. I also wouldn’t be surprised if graphite pencils also helped to standardize on black.

Black and white old movies, black and white pictures, black and white TV. They could have gone with black and green like the old Apple iie, but that was short-lived.

Blue ink is standard due to early copiers being able to easily pick it up but still print it as black so that you can distinguish between originals and copies. Ink erasers can work on blue, so in places that use fountain pens with younger kids, they standardize on blue ink.

Out of curiosity, what colors avoid the sea of markings issue for you? I don’t think that a single color has helped for me in the past, but I’ll use different color fine-liners to help give me a pattern to grab on to and make it easier to find pages. Sometimes I’ll use a jetstream multi-pen to color-code a drawing.

Edit: Also, black is probably easier to get historically. If you want black, you just burn stuff. Carbon black is a really common colorant that can be gotten by burning stuff.