I think the fact that the SNES hardware is proprietary would make it very tough to catch all the corner cases (since we'd be reduced to tons of test and check cycles or using SEMs to examine the chip).
Plus, many cartridges has supplementary chips, so the fpga would also have to include all the different chips used, and all these are proprietary as well.
But all the hard work is done: bsnes emulates all of those chips. Sure, it's not trivial to convert bsnes to vhdl, but there's no need for further reverse-engineering unless you want to make pin-compatible replacements. The bsnes code and documentation contain all the information necessary to make an FPGA into a SNES-on-a-chip.
Plus, many cartridges has supplementary chips, so the fpga would also have to include all the different chips used, and all these are proprietary as well.