I find cheating to be okay, so long as you're keeping it personal and not letting it affect others' experience (for example, hacking some Pokémon, and then trading it with a stranger). I've never had to go through such a thing, but I'm sure plenty of other people have, and while some necessarily don't mind, others definitely do; if you're not careful as to what you're doing, hacking Pokémon could indeed make them seem illegal. If you are, though, and manage to make them look and behave like a legitimate one, then I suppose it won't be such a huge issue.
Do I cheat, personally? Yes, I do. I don't cheat throughout my initial play, but when I give the game a second or third run, I find myself trying them out every once in a while just to see how it's like. I'm a huge fan of walk-through wall codes, as they allow you get to places that you never could before, by enabling you to, as it says, walk past anywhere. It's pretty fun, actually!
