Copyrighted content and pirated material have never been allowed on GitHub. If you're trying to pirate stuff off of GitHub, you're doing it wrong.
That said, I get the feeling that OP is referring to emulators, CFW, and ROM-Hacking tools; those have always been legal, despite some intents and implications hiding behind them, as they don't explicitly contain any copyrighted content in their repositiories. They merely utilize and manipulate existing copyrighted content. How said content is obtained is ultimately the responsibility of the user.
While I don't entirely trust Microsoft, their recent open-source initiatives and now their acquisition of GitHub seem to be PR moves with the open-source community. Zapping emulator repositories would be counter-intuitive, and ultimately detrimental to their image. That's not to say that doing so is above their standards, and that they might not do it later on down the line, but, strategically, it wouldn't make sense. Emulator and CFW devs should be fine.
Besides, I'm sure they've heard of SourceForge, their anti-developer practices, and the site's ultimate fate, so I'm sure they're going to try to stay on good terms with as many users as possible.