JJ --
Fwiw, SuperDuper! is, afaict, smart enough to copy only the changed files within the Library. At the same time, it still has to read all the files, and this can take as long as it takes Finder to simply copy the files.
I set SuperDuper! to run when none of the Libraries or machines are in use (viz.: overnight), and to update sparse bundle files of every Library and every set of Referenced Originals. I only do this once per week, however, on alternating back-up drives. I back up all critical Libraries every day using Time Machine. (TM worked _poorly_ with early editions of Aperture 3.x. It has become usable -- kudos, I guess, to Apple's engineers.)
I administer one very large and unwieldy Library (finishing the upgrade to 3.3.x took 170 hours of full-on processing on a 5,5 MBP). I'm just getting to the point of setting this back up for back-ups. I will be looking at efficient ways to do this. I gave up on Vaults long ago -- I couldn't get consistent results on any Vault over 50 GB (iirc). Afaik, this limitation has been removed in the most recent upgrades.
My biggest Library contains over 3 million files (not Images -- files).
Fwiw, I _think_ that TM now backs up at least part of open Aperture Libraries. Have not taken the time to pin this down, however. TM certainly exhibits much better behavior with Aperture -- but this may be the result of (programmatically) ignoring it.
So my suggestions:
- make sure your Vaults are working (verify!).
- see if SuperDuper! is better are updating back-ups. (Iirc, a trial is available.)
I am semi-happily running a rMBP, and may move all external storage to USB3 or T-bolt. As it is, I can't sell my old MBP until Apple releases the Firewire<>Thunderbolt adapter. (Yo!!) I am not savvy enough about hardware to know if the faster bus (is it the bus?) will increase overall performance.