> Does it matter that GitHub themselves is not open source?
It matters a lot actually; a lot of free-software/open source software are licensed that way because the projects themselves are ideologically predisposed.
While that does not hold true for certain (even large) projects like Linux, it certainly holds true for Apache (historically) and GNU.
To put it another way; if you found out GNU coreutils were hosted on Window machines using IIS web servers then you would probably consider that the people making the software (or, certainly those hosting it) are ideologically at odds with the project and are hypocritical.
So, I mean, you get to choose, if you go the Linux way and say "we are open source for pragmatic reasons" then there's no doublethink. If you say "we believe that all software should be free" while simultaneously forcing your users to contribute using closed source software on a proprietary platform then then you're not practicing your ideology, and worse; you're forcing that non-practice on your developers and users.