Simple, effective answer: Yes, make copies of your Libraries as back-ups and don't use the Vault feature.
Vaults are no more than a back-up created from within Aperture. (I suspect Apple added this feature on the assumption that users of Aperture did not regularly back up their data.) They can be problematic (they can also be problem-free). If you are comfortable with Finder or with a program such as SuperDuper or CCC, use it and don't bother with Vaults. (That's what I do, and that's what other top posters here do as well.)
As far as data back-up goes, I recommend that all users maintain at all time three copies of their data. A working copy, a copy of the working copy that gets regularly updated (no less than once a day, unless the data is unchanged), and another copy of the working copy that is kept off-site. Never have all three copies in the same physical location (don't bring your off-site copy on-site. Take your on-site copy off-site, and then bring the off-site copy on-site, effectively swapping them while never having all three copies in the same location).
As for making on Library for each project ... it is generally not recommended. One of the great empowerments of Aperture is that it functions as an index of all the work it contains. I have _every photo I've ever taken_ in my personal Library. I can search my entire oevre. Your needs may be different -- and may be different enough that making one Library for each project you do is sensible -- but using separate Libraries takes the power of this global indexing away. (Fwiw, the reasons I can think of having separate Libraries: image security, image quarantine, multiple photographers, and Libraries of images where the photographer is not important.)
HTH,
--Kirby.
(Sent from my magic glass.)