FTDI isn't just 'not supporting' counterfeit chips, they're actively trying to prevent them from working.
Nothing wrong with that. People shouldn't use counterfeit chips. As soon as they discover that their device stops working,
blame the seller of the device. Not FTDI.
And yet that is not happening. People can keep yabbering on about managing their supply lines, complaining to suppliers, etc but the fact is that is taking extra effort one way or another so companies are going for non-FTDI chips because it is easier and thus cheaper for them. It is all about the economics of doing business. Companies don't care whether FTDI is right or wrong; they just want to order a bunch of USB-UART cables from their supplier in China and be done with it. These kind of cables are usually not their core business anyway so less hassle it better.
In the short term it is easier and cheaper. However, with the grown popularity of alternate solutions such as the CH340, it is only a matter of time this will be counterfeit as well, which imposes an unknown scenario - i.e., this device can fail in yet
unforeseeable scenarios.
Therefore, in this case the scale goes back towards FTDI: counterfeits (or most of them) now fail in a
deterministic way, which raises the accountability of the supply chain.
For companies that are
actual semiconductor company customers - i.e., use their devices in their products - the early detection of fakes is taken into consideration very highly across the industry, either via visual inspection or, in this particular case, functional inspection. Just as anecdotal evidence, I know companies that use FTDI devices in their products and will not do a redesign for this factor alone but instead take into consideration the whole solution such as availability, OS drivers, support, etc.
Obviously that, for companies that need accessories or purchase finished board through third parties, this can become a nuisance that can be worked around in several ways, including but not limited to the proposed change in specs (imposing a specific device supplier).