I was able to get nnid working with 3 o3DS units by:
Downgrade sysnand.
Create rxtools emunand.
Update emunand from system settings. (in your case, update to 9.5 manually on n3DS)
Unlink nands by formatting sysnand with SD ejected.
Update sysnand to 10.3, link existing nnid, login to eshop to...