While that definitely would prevent piracy, they won't do that. That would mean you'd have to connect to the internet the first time you use a game, and that would be stupid. Like when I got Smash Bros 3DS, I was playing it before I even got home. And suppose you for whatever reason can't connect your 3DS to the internet or something, then you wouldn't be able to play any games. It seems that Nintendo doesn't think that everyone with a 3DS has internet, since they don't like to use internet features much or require them at all. And some people don't use their 3DS at home but only during travel and such, that would be quite a burden to them if they forget to register their game or something and can't use it.
Considering Nintendo's heavy *HEAVY* reliance on social features like streetpass and such, and the fact that wifi hotspots are basicly found in every streetcorner nowadays.
It should not be impossible for the majority of their users to get that access.
The question is, is Nintendo willing to alienate the users that live "in the middle of nowhere" or otherwise can't verify.
Though there are other similar verification methods that could be used in a similar fashion.
The point is, Nintendo could implement something that would prevent a feature from working.
Which is why Gateway mentions "don't update beyond 9.2" - even if ODE would mean they would theoretically work on all versions. (And its mere speculation that that may be the method used, alongside the 9.x theme theory.)
As always, update at own risk and all that.