I hate to be the bearer of bad news, but it sounds like your instance has been compromised by a malicious actor exploiting CVE-2021-22205 which affected GitLab versions 11.9-13.10.2.
The fact that a miner is targeting your system suggests that the system is vulnerable and has been compromised. I suggest you check here for indicators of compromise.
The missing repositories sounds similar to this. If your repositories have been encrypted or deleted by a malicious actor, I suggest you spin up a new server, install GitLab, and restore your latest working backup to it.
If it is the case that your instance has been compromised, we’ve shared some suggestions to help mitigate further threats here.