Hello,
The API will not return entries that are deleted [status 3 in the kaltura.entry table].
When you say "there are rows in the entry table that you can't query for, by ID, using the API. The API simply returns no results" do you mean entries where the status is different than 2? if so, that is expected. If you mean entries that are in status 2 in the DB and still do not show when making the API call, that is probably because they are incorrectly indexed in Sphinx. This can be fixed by running:
# php /opt/kaltura/app/deployment/base/scripts/populateSphinxEntries.php