You realize reverse engineering is legal and actually protected by law right? Tampering with other vendors' computer systems is not (in the software world that's called maleware).

The "counterfeiting" issue is a trademark problem only. In other words, the only thing wrong here is that the Chinese manufacturer stamped FTDI on their chips. There's nothing in trademark law that says it's OK to use these tactics to combat the issue. Why would there be? The two are completely orthogonal to each other. If there are chips out there that emulate FTDI and do not have the logo, FTDI has most certainly broken the law. As others have pointed out, this would be like Intel damaging AMD chips simply because they identify themselves in a similar manner. (again, minus the bit about trademark which is again, orthogonal to what FTDI has done here).

Someone reverse engineered FTDI driver on the EEVBlog forum and its not specifically detecting fakes. Its doing EXACTLY SAME procedure without discrimination - it is issuing illegal (and ignored on real chip) write to eeprom.

There is no detection, just some fuzzing with illegal instructions.