There are a number of external thunderbolt PCIe chassis around and some interesting new ones on the market soon.

Not all cards are compatible though - drivers need to support thunderbolt connectivity and there is certainly a limit to the number of cards and bandwidth available - even with the next generation of thunderbolt.
It's a bad idea to speculate until its all released and fully tested.

The new MacPro has a good spec and interesting design, but the form factor is not ideal for our purposes...

It's just a pimped mac-mini really... The 'Pro' name should be removed

S