By taking down youtube-dl, Github has opened a window for copyright trolls to speculate about what a repository is used for, and take it down if one of its use cases involves downloading copyrighted content.
I can see how it's legitimate to take down a repository with the sole, explicit goal of downloading copyrighted content, but youtube-dl is widely used by journalists to preserve uncopyrighted content.
Youtube-dl is used by some journalists. Generally, most journalists at a real newspaper or media organization would ask for the original video, not a copy from youtube.
Even your local evening news will use the original video unless they are specifically discussing the online version of the video, in which case they will either record footage of the screen using one of the hundreds of cameras they have lying around or just share their screen view directly.
The only time journalists use youtube-dl for reporting is when it is not possible to get a copy of the original.
In earlier HN threads about this youtube-dl takedown, it was pointed out that sometimes authors of videos used youtube-dl to download their own videos, because they don't keep their own original; treating YouTube as a repository for their data, much like people use Google Drive, or GitHub.
So even when a real newspaper or media organisation asks for the original, those authors needs youtube-dl to retrieve that original. Or maybe they'll just tell the media organisation to download it themselves as there's no difference.
How? Virtually all content is copyrighted; the journalists would need to be restricting themselves to some very narrow topics like "government documents".
I'm not aware of any notices filed against that specific project.