Faster 2 TB external drive throughput?

Question

Hi.  I'm a heavy user of Aperture, and am looking for ways to overcome system waits (spinning pinwheel) when using very large Libraries.  The system waits happen when making adjustments, loading containers, and always when emptying the Aperture Trash.
The Library in question is all up-to-date and has been recently repaired (I run "Repair Database" on all Libraries as part of regular maintenance).
My System:
MacBook Pro
Retina, 15-inch, Early 2013
Processor  2.7 GHz Intel Core i7
Memory  16 GB 1600 MHz DDR3
Graphics  NVIDIA GeForce GT 650M 1024 MB
System Drive  APPLE SSD SD512E
For this discussion, let's say "very large" for Libraries means >500 GB and/or >250,000 Originals.  These large Libraries can have millions of files in them.  (I've seen Libraries with almost 9 M files.)
Because of their size, I keep these Libraries on external drives.  Due to cost, I put these on USB-3 drives.  (I do have two powered USB-3 hubs.  I have tested using no hubs, and found no difference.)
I am running Aperture 3.5.1 on 10.9.3.  Smaller Libraries, whether stored locally or on external drives, work flawlessly.
Blackmagic Disc Speed Test gives me a rating of 370 MB/s for my SSD system drive.  The ratings for my several external USB-3 drives range from 50 - 70 MB/s.
Watching Activity Monitor (sad to report, I don't know how to use it under Mavericks to trouble-shoot performance issues) with Aperture loaded, I notice that it reads "Aperture not responding" when I get the spinning pinwheel.  ("Aperture not responding" has been common since 3.3 or so, and never, IME, indicates a hang or crash.)   Afaict, the problem comes from disk i/o.  Memory, however, is maxed out (typically, e.g.: 15.60 - 15.99  GB used).  CPU for Aperture sometimes get to c. 110%, but many times is at c. 10% or less when the spinner appears.
The Library that is giving me the most problems is c. 900 GB on a 2 TB drive.  The Originals occupy 1.75 TB on a second 2 TB drive.
Apple Store employees tell me a Thunderbolt drive will give me hundreds of of MB/s throughput.  I am skeptical because, afaik, USB-3 should give me up to 500 MB/s and I'm not getting anywhere near that (assuming -- perhaps ignorantly -- the the Blackmagic test is comparable to others).  A large TBolt magnetic drive has been recommended.  Will it make a big difference?
What can I do to eliminate the system waits? 
How can I better trouble-shoot what is causing them?
Will Thunderbolt be faster in practice?
Is there any way to get, say, >250 MB/s performance from an external drive holding a very large Aperture Library with millions of files?
Is this the best forum for this?
Thanks.

Answer 1

First problem most hard drives (Besides SAS 15k) have a throughput less than 100MB/sec.
Thunderbolt won't really help in throughput becuase the drives are already maxed out.
Three options for moving forward:
1. Making smaller libraries is going to really help fix this issue.
For reference, your large photo library is like reading the entire encyclopedia to the computer, it takes a long time to look through the entire database (book) to access the files Aperature wants.
When you make said libraries smaller, your computer can read the cliffnotes version in no time at all.
2. Get a Server or NAS that can do RAID 5 and with the right drives you could reach 300MB/sec.
But that's expensive. I've been able to max out a 1gbps(125MB/sec) link with my photo server while copying assorted photos between drives, but I have zero wait times when working with my images.
3. Switch to Photoshop or work with files natively on the disk, not inside a database.
Lightroom works on the same photo database principle as Aperature so I cannot recommend it for your case as you won't see any performance improvement.