The NES cartridges have a protection chip, the famicon ones no.
Some cartridges have ram o nvram, paging circuits, logic to enhance the graphics, audio generators somtimes. Suposedly are emulated by the emulator.
I dont known in snes, but in nes the protection chip only resets the cpu if it is no present, but does not encrypt the data. Of course, if the memory is paged, you must change the pages to copy all of them.
Aside, some prefer to use the real console because of controllers, nostalgia, etc. And if posible with a CRT.