Sycraft
Sadly MOTU are pretty Mactarded and so aren't likely to have good Windows support. You can have a Windows system with Thunderbolt, but MOTU loves Macs and have never had great Windows drivers. You might wish to consider an RME card. Though they operate over USB and Firewire, their latency is as low as anything you are going to see and their drivers are top notch. USB is actually not an issue latency wise, with proper drivers/interface hardware, most companies just aren't very good at it.
I just wouldn't recommend using MOTU stuff with Windows all that much because like I said, they aren't very good at it.
MOTU certainly is a bit Mac centric...
That said, the MOTU Ultalite AVB works great under Windows.
Round-trip latency can be set as low as 4.9ms at 44.1k.
FWIW, The issue isn't MOTU under Windows.
The issue is that PCIe over Thunderbolt isn't fully baked with Windows.
ALL Thunderbolt audio interfaces (not just MOTU) currently running under Windows are running Firewire protocol via Thunderbolt. Thus, there's no performance advantage vs. running connected via Firewire.
The reason you don't see the PC side rushing to support Thunderbolt:
Thunderbolt provides access to the PCIe bus (nothing more nothing less).
We've had PCIe slots for a long time. The technology exists, it's relatively inexpensive, and it works.
Other than the ability to connect externally, Thunderbolt offers no advantage to PCIe slots.
Thunderbolt peripherals tend to be a lot more expensive than their PCIe counterparts.
The reason Mac is pushing Thunderbolt:
The new "cylinder" Mac Pro models have no PCIe slots.
The only way to access the PCIe bus is via Thunderbolt.
IMO, Apple jumped the gun with this transition.
If you were running PCIe hardware, you now have to re-purchase Thunderbolt equivalents.
A much more graceful transition would have been a generation of Mac that offered both PCIe slots and Thunderbolt.
This would have given users more time to transition... and developers more time to solidify.
MOTU has shown that they can develop USB drivers that offer very low (rock-solid) round-trip latency.
I'm all about lowest possible round-trip latency, but 4.9ms (at 44.1k) is low enough to effectively work.
With quality PCIe card at a 32-sample ASIO buffer size, you can achieve round-trip latency in the 3-4ms range.
PCIe over Thunderbolt would offer similar performance under Windows.
The advantage of PCIe card or PCIe via Thunderbolt is the ability to effectively run at ASIO buffer sizes smaller than 64-samples.
Note that Core Audio under Mac allows lower round-trip latency than Windows.
This is not specific to Thunderbolt. You'd achieve lower round-trip latency with any audio interface.