It seems like Nintendo doesn't care about modders modifying their Classic systems.
I don't think anyone should feel that the 21 games already on there aren't enough-Super Mario World, Super Metroid, A Link to the Past, Secret of Mana, for example, are the cream of the crop when it comes to the wonderful library of SNES games. Online listings for the SNES Classic are bound to sell out nearly immediately, so don't count on getting one though those channels. So far, it has been noted that owners can fit in more than 200 games and even run other games using emulators.
Hacking the SNES Classic Mini, much like it did for the NES Classic Mini, means that you're able to load your own custom ROMs onto the machine and play them without issue. Furthermore, it entices consumers with the inclusions of the never-before-released "Star Fox 2" exclusively on the retro console. Games like "Zombies Ate My Neighbors" are beloved, yet they're sadly missing from the Super NES Classic Edition. The SNES Classic has nine games less than the NES Classic, and it costs $20 more. Nintendo also said, "In addition, more units of Super NES Classic Edition will ship on its September 29 launch day in the USA than were shipped of NES Classic Edition all past year, with subsequent shipments arriving in stores regularly". Among the trademark categories applied for is "video game system or program", which would fit perfectly with Nintendo's Classic Edition lineup of consoles pre-loaded with games.
NeoGAF user Robin64 has uploaded a step-by-step guide on how to hack the SNES Classic, but do keep in mind there's a grey ethical area with accessing ROMs without owning their original cartridge counterparts.