I think your question and concern is a very legitimate one. Im surprised no one has offered feedback of any significance.
I, myself, started asking your question back in December when I decided to get a new Mac Pro. Currently have a Mac Pro 3,1 fully loaded with 4 HDs , a graphics board, and several external HDs.
I did a mess of searching around for information as to how best to have external devices attached to the nMP but little if any existed. Finally, I decided to ask myself some basic questions about computers to arrive at issues which were important to me. Some examples of these issues were:
1. I want quality in whatever I attach to the nMP (I mean Im spending a wad of money for a quality machine, but lets be realistic, its minus any internal expansion).
2. I want speed since in 2 words the nMP is about power and speed. Consequently USB 2 connections will not cut it; its thunderbolt preferably or secondly USB 3.
3. I want silence on my desktop.
4. I want a minimum of clutter.
5. I want style and parsimony to match the nMP.
I decided to go with Other World Computings Elite Pro Dual Thunderbolt. I bought the bare enclosure, but you can buy them with installed HDs. The HDs can easily be set to RAID-0, RAID-1, RAID Span, or as Independent Drives. Im going to put 2 of the current HDs I have in the Mac Pro 3,1 in the Thunderbolt enclosure and use them as Independent Drives.
The connections can be Thunderbolt or USB 3. This setup solves a major concern of mine of moving HDs from the inside to the outside of the computer. The other HDs which are inside the Mac Pro 3,1 I use as backups, so speed is not that important, but it is still important.
Consequently, what I will be doing is connecting them to two devices by Newer Technology (also sold by OWC; I currently have these devices):
1. Newer Tech Voyager Q which is a hot swappable drive docking station: the basic version is c. $72, is USB 2 & 3, and can be used with 2.5 & 3.5 SATA drives.
2. USB 3 Universal Drive Adapter which can be connected to 2.5, 3.5, or 5.25 drives (c. $30-40).
Currently, I have a RAID 1 setup for my important external backups (NewerTech Guardian Maximus). It has served me well and I will simply be transferring it over to the nMP connection.
Youve probably figured out Im partial to OWC, but why not; they have not let me down.
If you want to connect PCIe cards, then go with OWC Mercury Helios Expansion Chassis (a little more expensive at $350).
The one device I have not settled on is a Thunderbolt dock to connect various other types of connections ( e.g., HDMI, Ethernet, firewire, dvi, etc.) to the Thunderbolt nMP. From what Ive read, reliability is still an issue but several vendors do offer them (e.g.,Matrox, Belkin, Caldigit). Hopefully in the near future a reliable, quality Thunderbolt dock will be built.
Thats my two cents. Wish you success in your quest and adventure with the nMP!