As long as you don't try to pass off the cheats to someone else who wouldn't cheat.. I don't really think its such a big deal, it only hurts yourself.
I have both diamond and pearl and an AR, but I don't cheat on pearl, which is the one I use on wi-fi to battle/trade. Every pokemon/item/etc I have was ligit traded or caught by me on pearl, but diamond.. well its just eh I'm bored I'm gonna just mess around XD
To me, if you cheat yourself then that's just you, but if you try to cheat others thats when it becomes wrong.