But when they were specifically revamping all the character designs to properly rep other games, why make two redesigns for BotW (one that doesn't even make sense) and then make another redesign for a game already repped (redesigning Dorf to Ocarina, when Young Link already had that covered)
It's just that MM was the most logical game for Young Link to represent since it's the one where this version of Link did the most and most differentiated himself from other Zelda heroes. Even with how he plays in Smash it makes more sense since it's the game were Young Link actually had a hookshot and fire arrows.
Adult Link is really the only one who represents one specific game from Brawl onward (he also really needed those changes to step out of his speedier brethren's shadows, they outclassed him at everything he tried to do). Toon Link may have the Wind Waker in one of his taunts, but he is still replaced by Alfonso on the Spirit train and his Classic run in Ultimate is based entirely on Triforce Heroes, to say nothing of Four Swords references in the past. Likewise I do not think they view Young Link as strictly from Ocarina Of Time, because they use the Termina Field remix in his video on the Smash website, and way back in Melee they made a point to mention that Link has traditionally been depicted as a youth, so he is likely representing all classic depictions of Link as a whole. Nowhere is this more evident than NES Link being represented by him in red. They probably just use the OOT design because it is iconic, and to give Smash players something familiar to what they had before with Link.
And besides, there is Hyrule Warriors, a dedicated Zelda fanservice game with no restrictions on how much Zelda content they can cram in without being accused of favoritism for the most part.
Edit: Should we throw a fit if they don't include alts for Shantae representing each specific game of hers? Colors seem more fun to me.
As well as what Toy said, with regards to possible shadow announcements.