Hacking items is usually safe, so long as the items are actually available in game and you don't create them in unrealistic quantities. Like, I've heard of people being DQ'd for having 999 Masterballs, but if you hack in one Masterball, it shouldn't be a problem. As a general rule for myself, I never hack in items - I only use codes that change the quantity of an item I got legitimately in-game, just to guarantee that there are no problems.