Confirmed for Karmic, mlocate 0.21.1-2.
It appears "-e" is always assumed for non-native filesystems:

- "mlocate" will correctly find non-existing files on an ext3 filesystem, and 
correctly suppress them with "-e" enabled.
- for vfat filesystems (and probably ntfs-3g, too?), non-existing files are 
*always* suppressed. This is not only the case for individual files that have 
been moved/removed, but also if the filesystem is unmounted.

-- 
mlocate can't search from database file for unmounted drive
https://bugs.launchpad.net/bugs/382330
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