Toon Link not being in the Wind Waker chapter makes sense when you consider how despite (sort of) being playable via DLC the OoT, TP and SS incarnations of Link and Zelda don't factor into the plot at all. It's always the Hyrule Warriors version.



If Majora's Mask had gotten a story chapter chances are Young Link wouldn't have gotten a part in it either despite the relevance to MM.



EDIT: Though I guess Tetra throws a spanner in the works there, since she's WW's Zelda and more or less that game's answer to Sheik. Could've been they felt there was enough separation between Zelda/Sheik character-wise to have Tetra be her own character in HW's plot but not for WW's Link.