The majority of the clones are using "NES On a Chip" or "SNES On a Chip" - they have the same issues as the original minimal requirements based emulators and are generally quite quirky.
As mentioned in other comments, some SNES cartridges themselves contain coprocessors and other hardware. A clone console doesn't need to do deal with this since you're still playing physical cartridges (versus pure software ROMs).
But clone systems do have issues with many games anyway...
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Replicate each component of the original SNES hardware? That has been somewhat done: you can buy hardware clones of the SNES in many stores.
The majority of the clones are using "NES On a Chip" or "SNES On a Chip" - they have the same issues as the original minimal requirements based emulators and are generally quite quirky.
Though it looks like at least one person is attempting to create a better one using FPGA: http://cegt201.bradley.edu/projgrad/proj2006/fpganes/
Yes, or replicate all of the original SNES hardware in one FPGA chip (and perhaps a few external passive components).
Citation needed, but pretty sure I heard of compatibility issus that the clones had.
As mentioned in other comments, some SNES cartridges themselves contain coprocessors and other hardware. A clone console doesn't need to do deal with this since you're still playing physical cartridges (versus pure software ROMs).
But clone systems do have issues with many games anyway...