Just swap the connector or make an adapter for the 2 player SNES to use NES pads. They both use the same IC's.
That would work, but your button numbering is going to be completely off (I think nes A and B is snes X and Y and there are a few others) and probably all of your extra buttons are going to be stuck in the "on" position with a nes pad plugged in.
It's worth a shot though... you can buy nes sockets for as little as 2 bucks... they seem to be the only retro connector readily available.
You make it sound like a big deal

IIRC A becomes B, Y becomes A, the rest of the button mapping is identical, which is what counts.
As for "extra" buttons being "pressed," so what? Any decent emulator that will easily let you to remap a controller will also easily ignore those buttons.

If you're really anal about that, might as well crack open the controller, cut the ground to pin 11 and add a pull-up. But if you do that, you can swap the cables from a dead SNES controller.
TBH, I see only two things you need to worry about. Whether the adapter has some sort of internal functionality associated with those bits and whether the emulator is unable to remap buttons in order to reverse the AB layout.