This is nonsense. There are literally dozens of potential exploit vectors in almost all games on 3DS (a couple might have only a few vectors). Each individual vector could take hours to fully check for vulnerability. It is very easy to simply write off a potential vector because at first it doesn't appear exploitable, but if Nintendo were doing this, they would need to be completely sure so would have to check very carefully.
If they could do this, do you not think they would, regardless of neimod noticing the exploit? By which I mean, do you not think they would spend hours checking games for vulnerabilities before each one is released? (Hint: they probably do that already, but they miss some; no reason why they'd pick it up now when they missed it before).
Simply knowing that there is an exploit in a game won't help them in anyway; it would be much, much too great an effort to try and find the exploit with that little detail. Ifthey knew the game, they could probably have a few people work on it for a few days and find the vulnerability. With the entire 3DS library; not a chance. Would take months or years to check every game.