Clones didn't exist, but copying devices did. At the time, there were many third party copying devices that would dump any SNES or Super Famicom game that didn't require special chips to a floppy disk and therefore allow for illegal copies, sort of the predecessor to burning CD based games.

To get around this, many later SNES games began to include anti-piracy measures into their games if they detected any latency from the lockout chip to the system. For example, this happens with Killer Instinct, Donkey Kong Country 2, Megaman 7 and many others.

In the case of EarthBound, Nintendo was heavily promoting the game, and since Final Fantasy II and III were common targets of copying devices, they wanted to ensure EarthBound wouldn't be in the similar position. So rather than refusing to boot, EarthBound would place 2-4x more enemies in EVERY AREA making the game no fun to play, and if you did manage to get your way through the whole game, you'd have your game save erased by the final boss. Nintendo: the original trollface.