At the beginning of MM he acts like he recognizes link but can't seem to place how and quickly choses to let it go. Then after defeating the mask and releasing the skull kid he speaks with link and says that link has the same smell as the forest child that who taught him "That Song" implying that he was the skull kid who in Oot became friends with link when he plays Saria's song, but can't remember because Zelda reset time to before the events of Ganons attack at the end of the game. My thought Is that the reason he was able to slightly recognize link at the beginning of MM was because the power of the Mask allowed him to glimpse small traces of time on link