Part of the issues to consider is that If you use GitHub issues, having multiple repos you may need to enable issues in multiple places. This means more to manage and track. Having all issues for multiple repos on a single github repo also has issues.
There would certainly be some scalability issues. The Mynewt project, for example, has many repositories. I can find the page but I recall that it is on the order of a dozen or so repositories. NuttX was, at one point, five repositories. We currently have four (excluding the three or four additional non-Apache support repositories)
If the number of repositories becomes large, it is hard to imagine any practical way to manage all of the issues with github issues.