What i think is that only link and zelda know about this, and decide to keep this as a secret ,and then maybe later the people find out about the trouble that link and zelda saved them of, so link spends time in hyrule in his youth like months top, but not years, and link decides to go look for navi, and zelda once again gives him the ocarina of time for his journey, is because she thinks she's not responsible enough or something, and malon gives link epona for his new quest of finding navi, because it is navi who he's looking for in majora's mask, that's his invaluble friend and the reason navi left was because the old deku tree died and it was her only parent, i guess