Look at how counterfeiting laws work for money. If you pay with a $100 bill in a smokey bar at night and get a $20 counterfeit bill in change, and don't realize it until the next day, you're out the $20. If you try to spend it, you're actually committing a felony - it doesn't matter if you printed the phony bill yourself, or if you just accepted it as change and are passing it forward. It also doesn't matter if you realize it's counterfeit or not, although the Secret Service agents may agree to give you a pass the first time you try to spend phony money if you claim you didn't realize it was counterfeit, and cooperate completely.
However, currency counterfeiting laws are very specific to money. Let's look at product counterfeiting, which works similarly but probably without the felony charges.
If FTDI discovered a container of devices with counterfeit chips was en route, they could tell Customs, who would order the contents of the container to be destroyed once they arrived on the dock. This would be a problem for the shipping company, who accepted the devices for shipment and never delivered them, so they would have to pay out an insurance claim. The insurer then has to deal with the liability by going back to the shipper and saying "hey, your devices were destroyed by Customs, I had to pay out for failing to deliver the goods." I expect the shipping companies deal with this all the time, though, and have a contract clause that absolves them of insurance liability in this case. In this case, the supplier is out the money. Their recourse would be to go back to the manufacturer and ask for their money back. Maybe the manufacturer will honor the request, maybe they won't.
If FTDI discovered a shipment of devices with counterfeit chips already went to MicroCenter, they would call the Secret Service, who would contact MicroCenter and MicroCenter would have to pull them off the shelves and destroy them, leaving MicroCenter without the money. Their only recourse would be to contact their supplier and say "hey, you sold us counterfeit goods, we want our money back." Maybe they'd get their money back, maybe they wouldn't. It's a risk.
So FTDI has now found a way to destroy a consumer device. As above, the consumer is similarly out of luck. Their recourse is to go back to MicroCenter and say "hey, this adapter, it's broke." Maybe they'll get their money back, maybe they won't. It's a risk. MicroCenter might eat the losses, or they might go back to their supplier, who might go back to the manufacturer.
In every case when the counterfeits are discovered they are destroyed, leaving somebody without the device and without the money.
I think FTDI may have a pretty solid legal ground for behaving like this, even though it's always a crappy experience to the person who got stuck with the phony. The main difference is that FTDI is doing this without asking the Secret Service to investigate the counterfeits first.