I am also wondering if you've personally had success with a GPU card in any Thunderbolt enclosure. Sonnet does not list any GPU cards as compatible on their website list.
Also, in talks with Magma last week, it was clear that they are looking for some engineering support partnership in an attempt to solve the GPU / thunderbolt driver issue for their ExpressBox 3T. They told me that it's Apple that hasn't allowed the support up to this point, and perhaps they're trying to find a work-around. But a GPU should work fine in Win7 under bootcamp.
I will be in San Diego with Magma doing tests all day this Friday on a variety of cards and applications, so I hope to report from practical experience soon after.