Well it's a hacking device, so yeah there are usually side effects when you alter the code the game uses

But since the games are saved on memory carts, simply make sure you have a "backup" memory cartridge that you use for codes/modified games, and a main one that you use for non-modified data.
Since the gamecube hardware/software is unchanged, and the game data is stored on disc, you'll never "permanently" have an error/side effect. Since you're directly modifying the game data, though, you could corrupt your data, so it's best to not do it with your precious gamesaves.
Another reason why removable memory is better than a HDD!