The only problem I can see is that you will have an issue powering the
relays directly though the buttons. The on resistance of these button can be quite high and is unlikely that they will
power the relays directly. In this case you will need a seperate relay driver such as a transistor or the ever so popular ULN2003. You might also need to debounce your buttons, but that really depends on the device you are trying to control with the relays.
About running 12v through the nes controller, are you just simply
applying power to the buttons, and not the internal circuit (if there is one).
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