If you are playing via an emulator like Citra, you cannot access the eShop directly. In this case, you need the update in a .cia file format.
By keeping your Pokémon Omega Ruby version current, you ensure that your journey through the Hoenn region is smooth, glitch-free, and ready for every online challenge.
Dumping your own: The most legal method is to dump the update file from your own physical 3DS using homebrew software like GodMode9.