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If the complaint is to be believed, most of these weren't really 'projects' but just copies of the original source code.

The kind of copies one does to be safe in the case the original repo disappears for some reason. Ironic.

Usually using the "fork" option suffices... these changed the original repo to remove GPL and such.

According to the notice, they were unchanged or mostly unchanged forks of the master.

I presume one wouldn't strip copyright in those cases.

They didn't. The master repository did, they probably weren't aware of the issue.

Thank goodness GitHub doesn't employ the YouTube 3-copyright-strike system. Otherwise there would actually be an issue with this.