Confession contains spoilers about Shugo Chara.
Since the confession is under a Read More, I’ll put my thoughts on the confession under a Read More, too.
…I actually didn’t think it was so random, especially Nagihiko and Rima. There was plenty of small hints throughout the manga that the two had something going on between them. Rima was often tsundere towards Nagi, and Nagi really wanted to get to know Rima.
As for Kairi and Yaya…They didn’t have as many hints, but in the scene when Kairi was going to leave, Yaya was really upset about it, she was crying and everything.
Of course, regardless of all of that, I also think that: just because Nagihiko and Rima got a chapter together and just because Kairi and Yaya got a chapter together that doesn’t mean that the mangaka were trying to say, “Yes! They are now canon pairings, shippers!”
The series was dealing with a bunch of elementary and middle aged kids…The main character doesn’t even end up with anyone right then and there (I mean, her future relationship was largely implied, but nothing was concrete and put into stone when it came to her love triangle), because she is still very young and uncertain about love, romance, and etc.
And so, while both of the extras could be taken as indicators for possible, future romances between Nagihiko and Rima and Kairi and Yaya, those chapters were, essentially, only about establishing friendships between these sets of characters. And in the case of Kairi and Yaya, that was necessary, since they were going to be in charge of the Guardians come the next school year. So they needed to be closer friends than they had currently been.
Finally, even though Shugo Chara! Encore! did provide some closure for the overall series, it was mostly just a volume of omake. So, those chapters can be largely ignored or overlooked and it really doesn’t change the overall story or plot of the series.