Honestly most people who use emulation probably own a copy of the games they emulate. It actually is possible to legally obtain a ROM or iso of a Nintendo game, despite how bad Nintendo wants you to believe it isn't. You are allowed to back up software that you purchased. Do most people do it the legal way? Probably not. But effectively I think it's all the same.

Wanna make money off your old games? Release an upgraded version. Put in the content that was left on the cutting room floor and up the resolution. Or just sell it as an emulator pack with the bare minimum requirements for it to function on the console like they did with 3D all Stars. People will probably still buy it.