Aperture 3 t vs Time Machine

Vaults are from the time when Time Machine didn't even exist, and they stuck around. The there used to be a big size advantage for using vaults, because Time Machine would backup your entire library, by just opening Aperture. This disappeared with later 'versions' of Time Machine. Secondly, because the vault didn't include the previews (something that disappeared in Aperture 3) vaults where smaller then the entire library.

Nowadays there's only one consideration I can think of: Time Machine won't backup your library when Aperture is running. So if you leave Aperture open all day, use vaults!

About the apparently missing referenced files, is there a possibility they are trashed? And are you sure you have no other criteria then referenced in your search HUD?