History says you aren't going to be banned for cloning Pokemon. Cloning Pokemon has been commonplace for years and is rife within the competitive community. We can assume that the developers would prefer that you didn't abuse glitches, but they have only ever taken action against people who edited their save files – and apparently, that only happened to people who weren't very smart about their hacking. That's not to mention how difficult it is to prove that a normal-looking Pokemon is cloned or hacked in the first place.
Usually, the word 'illegal' is used in the context of competitions like VGC, which will penalise players for using 'illegally manipulated Pokemon', as described by the official rule book. However, it's unclear whether cloning Pokemon passes as illegal manipulation and, obviously, it says nothing about trading Pokemon. Some people will tell you that an illegal Pokemon is simply a Pokemon with traits that it can't normally access, which is different from a Pokemon that was obtained through illegitimate means, which is a more apt description for cloned Pokemon.
At the end of the day, the standing of cloned Pokemon depends on who you ask. Some people would be very upset that the Pokemon they received was cloned, and others would not care at all. If you're trying to be ethical, then I would advise against circulating illegitimate Pokemon in the Y-Comm, and I certainly wouldn't send cloned Pokemon in online trading forums with a legitimacy policy. But I don't think you have to worry about being banned.