PetrPomkla,
Is there a reason you're not considering the PXIe-8301? That allows you to connect directly to a PXI Express chassis.
Thunderbolt compatibility has several levels. For Windows, an uncertified driver will generally work during normal operation. From my experience with a limited set of (NI) devices everything works fine (hot plug, cold boot, etc.). I haven't tried sleep much, and everything is inactive when I unplug it. Hot unplug is the "riskiest" piece, though I haven't personally seen a problem with it. There are a lot of corner cases, so you could probably find something odd if you try.
- Robert