Having the option of motion controls is strictly better than not having it. Therefore, I believe that IF the motion technology is cheap enough to implement onto the joycons, it would be a no brainer to include it, due to the fact that the controllers: 1) are detachable and 2) have verticality to them, just like the Wiimote.
Also they will have to find a solution to the Wii Virtual Console future, or they would have to rework the controls for each release, which hurts some titles build around motion.
In other words, I think that the only reason Nintendo would NOT put motion on the joycons would be either: 1) Its technically impossible due to size. 2) It makes the hardware considerably more expensive to manufacture so its not worth it financially.
(TL;DR) What I believe is that it is possible and might be cheap enough that it could happen, but I would like to hear your thoughts.
Discussion started at here by OathOfRhino