Corrupting the actual data and game files on a cartridge through digital means such as cloning is almost impossible. Game data (but not the save file) is stored on cartridges as "read-only memory". This means that the game files cannot be modified, only run by the system. This makes them basically impervious to any possible modification or exploitation that can be done with save files, such as cloning. This is incredibly secure -- not even eShop updates to the game can modify the game ROM. Updates are instead stored on the SD card and run when the game is opened; this is why you'll need to install an update again if you use an SD card that doesn't have the update on it. The only thing that can be overwritten in the game cartridge is the small amount of flash memory used to store save files, which is at risk of damage if you use cloning or other exploits and glitches.
So your cartridge and the game data itself is at no risk if you use cloning exploits, but there are absolutely no guarantees that your save file won't be corrupted in the process. The only way your cartridge can be damaged besides through potential "hacks" is by physical means.