It wasn't that the chips were fake, they could only be fake if they claimed to be FTDI. They could have been merely FTDI compatible, at which point did FTDI have any grounds to destroy compatible parts?
What FTDI did, on the other hand, is malware and clearly illegal. It is destroying private property and I guarantee violated multiple laws in many countries.
Of course this kind of vigilante justice by FDTI is illegal, but who is going to press charges if that means they will get their devices taken from them and destroyed?