Yes. The administrator can unprotect any document protected by a user within the organization or by external users who have used company protection policies to protect it. In any event, in order to allow exhaustive access to the information for auditing, all of the administrator's operations are recorded on an audit log. This means that the administrator's actions can also be audited.
You can see how to unprotect any document in your organization here.
You can see how to audit admin actions here.