According to the Salesforce documentation on ContentDocument
Users (including users with the “View All Data” permission) can only query files they have access
I find this very strange. Why would a System Administrator not be allowed to see all ContentDocument records within Salesforce?
Is there a way to circumvent this limitation?
EDIT: The weirdest thing about all this is that the Admin user can see the ContentDocument in the Salesforce web interface.. but they can't be obtained through the API. That makes little sense. I'd expect the API to show as much or more data than the web interface, not the opposite.