Hey, at least I get to share with zhoutong the dubious honor of having had my name verbified by the forum users. I guess that's something!
Just guessing, but he probably daisy-chains the hashers in each clock region, runs them one step out-of-phase with each other, and has a single bram feed them k-values which get passed along from one hasher to the next, bucket-brigade style. My very first design -- which was bit-serial (really bad idea!) -- worked that way.
The DNA register is just a shift register; it's trivial to swap it out for an SRL32 in fpga_editor.
By the way, these guys have documented the bitstream format and made tools that turn .bit files back into .ncd files -- even (completely illegible) .v files in some cases.
I don't think Xilinx wants the liability that comes with being a certificate authority -- especially one whose certificates can't be revoked because they're burned into millions of dollars worth of silicon. You can bootstrap similar schemes yourself on Virtex-6 and above; see section 6 of this paper.
I wouldn't trust them if I were you. It's completely trivial to extract the AES key from Xilinx devices, even Spartan-6. Even battery-backed ram. Only one power-on is required, and the equipment isn't expensive (if you rent it it's downright cheap). They didn't fix this problem until Virtex-6.
Quite prescient of you -- stay tuned. But I'm not sure how well this would work for you -- with a highly-rolled design it's easy for an attacker to tell the difference between countermeasure circuits and the actual hashers -- just look for the pattern and chop out anything irregular. Once you've got it down to a few hundred slices it's easy to figure out where the inputs and outputs are and what they mean. Replicate that block, stitch it back together and the game's over.
On the other hand, you guys make your own hardware -- that's a big advantage when it comes to anti-piracy measures. You might be better off looking into ways to leverage that, like a tamper-proof housing around the spartan that erases the bitstream if breached and extra circuits to thwart power-analysis attacks. People are also less likely to try to reverse engineer your work if they have to take apart and possibly damage a box they've paid $100,000 for!