I completely agree, on the other hand, that a takedown notice issued knowingly without proper grounds should be penalised severely.
Regardless, I think they takedown without giving the "DMCA" complaint much scrutiny because the risk of penalty for NOT taking action is greater than just taking down the repo(s) risk-free.
Github's ToS: which says "we have the right (though not the obligation) to refuse or remove any User-Generated Content that, in our sole discretion, violates any GitHub terms or policies." ( https://docs.github.com/en/free-pro-team@latest/github/site-... )
I have to say it IS strange they took down content based on a letter that doesn't prove or even really suggest copyright infringement has taken place (only that it COULD, as a result of using the software), and their own ToS says "There may be legal consequences for sending a false or frivolous takedown notice." ( https://docs.github.com/en/free-pro-team@latest/github/site-... )
Except, by choosing to honor it, they decided that it is legally valid.
The appropriate response to a copyright claim against material that the claimant clearly does not own is 'unless you can prove that you own this material, come back with a court order.'