I guess the argument would be that software fixes need to be implemented for each ROM separately. Which also involves the pain of decompiling. Yes FPGAs are probably a pain, but they potentially offer perfect emulation of every game.
One thing I’m not sure about is how portable FPGA logic is. If I write a NES emulator in verilog for one FPGA, can that code be reused on a later model if, for example, my FPGA goes out of production?