So the NNID that is also banned after all, not just the 3DS?If you transfer from the banned 3ds to a new 3ds, the new 3ds will get banned too... So, any 3ds with that NNID will be banned, but you can use that NNID fine on a WiiU. If you get another 3ds, just don't transfer the banned NNID to it.
Because I still have my old 3DS lying around and if I recall correctly Nintendo does let you change which system the NNID is linked to if you call them. It wouldn't be a regular System Transfer, but this would mean that system would get banned simply by association, which seems kind of odd.