Nah I don't think the black crystals makes sense with what Anna's canon quotes are saying. I think it's more like, the hour glass will sit empty for a long time, until Gryffindor has won more points than they've lost. Say they earn 200 points in the next two weeks. Over the course of that two weeks, I think no rubies would fall into their lower hourglass until they've recouped the -105 and then earned at least one point more. You know? Just my two cents.

As for how the students can tell how many points they have... well, they don't exactly know just by looking. The hourglasses are just charmed to know.