Status command should report missing files.
When you run a 'status' command, it lists the files that are tagged and those that are not but it does this by examining the file-system and looking up each file in the database. If there are files in the database that are missing from the file-system (because they have been deleted) then these are not reported at all.
The 'status' command should report missing files with an exclamation mark (!) a la Mecurial.