Well, I agree that the "why" is important, I just know how the argument is probably going to go...
Personally, I don't think there's only one cause. I think there is probably an unfortunate combination of factors, but I think the most likely one has to do with economic disparities among black families since the nineteenth century. I won't even call this "systemic racism" - I'll just chalk it up to the historical contingencies of American slavery.
That opportunities for black graduate students exist doesn't necessarily mean that a wide number of black students are aware of such opportunities, or that their background has fostered any interest in applying to such programs. I think we see so few black graduate students because higher education, especially graduate school, resonates overwhelmingly with wealthy and upper-middle class families, and occasionally with students from lower-middle class families; and these tend to be white.