It is possible that the doc was deleted but remains in the analytics history. Are you not able to find it by ID in the jivedocument table in the operational DB?
Yes, it turns out the document was deleted and I do still see it in the jivedocument table. How do I know it's deleted? What I wasn't seeing was how to determine visibility, so I would still like to know that, too.
The status of a document is in the jivedocversion table in the core database. The states I have seen so far and their respective status IDs are:
deleted - 11, archived - 8, published - 2.