Correct. There are counterfeit ROM, RAM, and CPU of all varieties out there.

I wonder if it's possible to replace a ton of these really old CPUs by a combination of an FPGA, level shifters and a flash chip that contains a re-implementation of said CPU in FPGA bitstream.

Oh, absolutely, but it is usually way more expensive than buying a load of chips in the chance you'll get a genuine one. I work on a project called PiStorm that replaces the 68000 series of CPUs using a small FPGA for bus translation and a Raspberry Pi.

Yes, it's not only more expensive, but there are other considerations, such as power draw, heat generation, etc. that may be an issue.