In their business-continuity backups, you'd have to assume yes.
However, I would certainly be surprised if a Github support staff member went and fished out the off-site backup and mounted it to recover one missing repo. You'd hope that would require quite a few staff members to orchestrate.
But in general, yeah. Most engineers don't think about deletion very hard when they start designing a system, and it's also convenient (although with GDPR possibly soon illegal, situation dependent) for auditing and research to merely flag things as deleted and not show them to the customer. As a result, true data deletion generally gets justified away as a bit inconvenient and not really desirable anyway, and almost no software company really deletes anything on demand. Best you can hope for is semi-annual data purges to reclaim disk space.
If this bothers you, consider joining us in the world of self-hosting your services. Gitlab is in my opinion considerably better than Github anyway. Certainly it's worth spinning up a docker container and taking a peek around.
