Vaults back up only Libraries. Libraries do not contain Referenced Masters. Vaults do not back up Referenced Masters.
TM is one way to make back-ups (of any files). Vaults are another, restricted to Library files (which have the extension "aplibrary"). How these back-up tools fit into your overall data security scheme depends on too many variables to give even a rule of thumb.
I try to keep three copies of all data at all time, and never have all three in the same location. A reasonalbe way to do this is to shoot to a card, copy the card to your computer and leave the files on the card, then import into Aperture and leave the files on your computer. Then after you make a backup, you can re-format your card. And after you make a second back-up, you can delete the copy of the card files on your drive. At that point you should have one copy in Aperture, and two back-ups.
This gets complex with Referenced Masters, but remains -- if I can put it this way -- straightforward.
I use TM as my first and most frequently updated back-up of both my personal Library and my personal Masters. I used to use Vaults as a less-frequently updated second back-up of my Library, and stored it off-site along with a copy of all my Referenced Masters. I now do that just with Finder (my Vaults started to have problems when my Library grew to over 100 GB).
I manage some other Libraries which I back up regularly (and the Masters, separately) to external drives. I rotate these, and never have all back-ups at the same location. I do not use TM on these Libraries.