(This is missing the wider point, but regardless: AFAIK (do correct me if I'm wrong) git clone --mirror will not copy dangling references & those refs will disappear from the original after a git gc, whenever that happens.)

Human error is human error: sometimes people will do apparently egregiously stupid things if it's possible for them to do so, including things like deleting branches from a repository & then doing a git gc to "save space" shortly before realising that they weren't issuing commands to the shell they thought they were in. A backup strategy should be robust against dumb human mistakes as well as mechanical hardware errors, otherwise it's no backup strategy at all.

They say in the article that one step of the anongit sync is to delete projects from the anongit servers which have been deleted on the central server. If a user accidentally deletes a project, they should be able to recover it from a backup, but it doesn't sound like there are any backups.

The same idea applies to the individual repos themselves. A git gc will delete objects unreferenced by the reflogs, eg deleted branches over a month old by default. They say that the total set of repos is about 25GB, so it would be reasonable to keep at least monthly backups for at a year or more.