Yes, exactly.
I used to work at a sub-contractor for a large manufacturer of medical equipment, and all the systems we dealt with were like that. The device would run a very small embedded OS but would have a serial port for talking to a PC for firmware development, firmware updates, logging, diagnostics, etc. Their older stuff used real hardware serial ports, but their newer systems (~6-7 years ago now) were moving to virtual USB/FTDI serial ports, with an FTDI chip included in the embedded system.
These tricky FTDI drivers would absolutely have the potential to brick and/or alter the operation of such a device; it's not far-fetched or a flight of fancy at all.
I have a special interest in this thread/issue because I have recently been contacted by that manufacturer regarding one of these FTDI-using systems which has recently begun to exhibit new problems. I haven't started looking into that yet, and I don't know where it will lead, but I'll have to bear in mind the possibility of deliberate driver-based monkey-business now.
We already have fitness devices that can communicate with a PC. Is it really unthinkable that the next batch of medical devices will do something similar? For example, a wearable sensor to continuously measure your insulin levels?
Will you be using an FTDI chip in such consumer devices?