Umm, that's exactly how they got the keys: by downgrading a New 3DS to Old 3DS firmware 1.0. It's glitchy as hell when you do that, but it works well enough to dump the magical "OTP". I did it with 2.1 back in November 2015.
That 9.6 encryption that kept new3DS users stuck on 9.5? Yeah, we have the keys they used to generate that encryption.
I wouldn't rule out them having something sneaky up their sleeves, but for the time being we're invincible.