So far, the only difference in performance that's been documented is the power-down sleep current. And I don't usually mind using a cloned chip - I suspect I've never actually used a genuine FTDI chip. But the MCU is a bit different. If there's something that just doesn't work right, but it seems it ought to, could it be the fake 328P that's causing the problem? So it becomes another thing you have to rule out that you shouldn't have to worry about.
But I would guess the counterfeits work ok for most things or issues would have been raised before. When I tested the sleep current, it wasn't really the processor I wanted to test. It was the rest of the Pro Mini board, and to make sure I hadn't messed up something when removing the regulator and LED. And it was only when I received the second batch of Pro Minis from a different seller, which had been made with different parts in a different production run, but which also wouldn't sleep properly, that I began to suspect the processor. So I suspect there are many people out there using these chips with no noticeable problem.
I wonder what's being shipped now from AliExpress, Bangood, and the large Ebay sellers. My sellers were domestic US, and certainly not large, but could deliver in a week. SleemanJ reported receiving genuine parts on a recent order from TaoBao. So I guess there's a possibility that this was a single production run, and new stuff will be ok. Well, ok, just a possibility.
I still think we need Microchip to help find a reliable way for us to distinguish genuine from counterfeit.