Fair enough, communication could indeed be improved. NAL but I was under the impression that, while they could surely be more helpful here, once they received that official DMCA takedown notice they don't really have a choice in the matter of taking it down or not.
Well they said, I had 24 hours to remove the offending item according to the "remove sensitive data" link which I abided in a matter of a few minutes. They still took down the repo - that is the problem, not sending the notice.
"We're giving you 24 hours to make the changes identified in the following notice:
If you need to remove specific content from your repository, simply making the repository private or deleting it via a commit won't resolve the alleged infringement. Instead, you must follow these instructions to remove the content from your repository's history, even if you don't think it's sensitive:
Edit: disabling the repository after being notified by you within 24 hours seems to be against their own policy at https://help.github.com/en/github/site-policy/dmca-takedown-... - have you tried contacting their support again?