People need to stop asking "am I safe?" or "will I be safe?", no one knows. For all we know, Nintendo has some other way of detecting who has been pirating games. Obviously if they see you playing a headerless CIA and find out that your NNID has no license to that game, something could be flagged.
This whole thread is just speculation other than the fact that some people using public headers (which is MOST GW and Sky3DS users) got banned. There is absolutely no way of knowing if you're safe or not until we get some more detailed information, which probably won't happen any time soon. I've been playing my retail carts in classic mode and I don't even feel safe.
NO ONE knows if you're safe or not, just wait it out and see.