That was an option that he gave (towards the bottom). I have no idea if GH passes these on to the repo owner or not. GH may have just removed the repos.
If I didn't botch counting, there were 69 of them. Thats a lot of projects to deal with. Dealing with a single point of contact (Github's DMCA procedure) is a lot more efficient than dealing with 69 points of contact.
While I agree with you, if they went through the trouble to copy the code and strip out the obvious attribution and license information, I'd have a hard time believing they didn't do it with intent. I'm no DMCA fan but you'll have a hard time selling me that this was an honest mistake that is easily remedied via some friendly emails. But maybe I'm wrong.
But, the original author did give that option.