I was thinking about this too recently. Basically, it's irrelevant visual information so it is cloaked in black, similar to how interior roofs are in rpgs with a 3/4 top down perspective. To justify it, I guess the idea is that the deeper into the cliff/dirt/soil you get, the darker it is, until it fades completely into black, but some transitions are more abrupt than others.
I'm also curious about where the idea originated, can't think of anything off the top of my head. My preferred method would be to have a kind of strata system, with different layers of dirt/rocks/cliffs, where you can see bones and other misc. details down there, to make it visually interesting rather than stark in your face black. But of course, it is important not to get distracted with too many details in unplayable areas.