And when QA validates them on a set of systems that happen to be legit and ships it to systems that happen to have counterfeits?
You seem to be arguing in this thread with a false dilemma between EITHER we must accept counterfeiting OR we must brick the chips, but there are in between measures that are way safer.
Prior art: Several versions of Windows have been able to detect if they were "genuine". Non-genuine windows did not brick their machine, or destroy themselves. Quick googling suggests it blocks you from getting updates, and pops up with links to a page on Microsoft where you could properly license it with some discount. That exact solution may not apply here, but there are options other than destroying hardware that is carrying your name.
(I mean, this isn't even good for FTDI... how many customers will never find out about this and simply learn that "FTDI chips spontaneously die a lot"? Not the brand experience I'm looking for!)
FTDI does not provide any guide lines to third parties how to test whether their chips are counterfeit or not.
The only way to test it is trying to use it with FTDI's Windows driver, and FTDI randomly changes the both the detection criteria, and the action done on detecting a counterfeit chip – sometimes it bricks them, sometimes it sends gibberish, you have no way of knowing beforehand. FTDI doesn't even guarantee that this behaviour is deterministic!
As far as I understand, this "behaviour" is totally deterministic and certain. You immediately notice the problem in any test system.
Don't believe that safety-critical devices are allowed to install some drivers willy-nilly!