I think it's because he only appeared in Ocarina of Time and Majora's Mask... Call me out if I missed a title there. Toon Link has been in many more games, and I think Toon offered more differences in his moveset while still maintaining the Link in him. Young Link would be a great addition in Smash 4 if he could transform with masks... But seeing characters like Zelda and Shiek being split, I don't think Nintendo is very fond of multiple forms.