And as you say, the growing popularity of GitHub gives us all kinds of cool data even when there's no central package manager for the language. In fact, we're mining imports of every Python and R project on GitHub right now to build out the dependency network beyond the (much much smaller) CRAN and PyPi networks.
The idea with Depsy has been to launch quickly with two languages, so people could see what it looks like, then iterate and add more as we get feedback. So we'll count your comment as +1 for C and C++ :)
You have to start somewhere, and if you get GitHub working then it would be (hopefully) much easier to then include BitBucket, GitLab, etc. Indexing self-hosted repos would be pretty tricky, I imagine, if only because you'd then need to maintain a list of all of the servers to clone from.
Further, there's also the challenge of including software from all of the research groups who don't even appear to use version control, or if they do it's locked away on a private server or service. How does one attribute authorship rights to those people without source history?
Anyways, this is a long ramble now, but I'm mostly trying to illustrate that it's difficult to do what Depsy does with software when it's written in languages without a canonical package repository. That doesn't mean they shouldn't try to expand their reach just because "GitHub isn't enough."
Of course, if it's not a public server then you can't do anything, but then again in that case the authors can't really complain they don't get any credit for what they do.