I find it weird that Spirit Tracks takes place only 100 years after Phantom Hourglass. That means that it's actually possible that two Links were alive at the same time, right? Like even if we say Link in Wind Waker/Phantom Hourglass is ~15, and in Spirit Tracks he's ~15, then that means ST Link was born 85 years after PH takes place, oh, eh no that would make PH Link exactly 100 when ST Link was born. That's cutting it pretty close for a reincarnation! Link could have literally been his own grandfather from PH to ST hahahaha
There is also the whole thing with gramps from A Link Between Worlds, for some reason on the game ending credits there is a whole scene with him as the center and with the main zelda theme playing, plus he is an optional boss as a shadow link battle and he is a 100% maxed link (all hearts, best tunic, best shield, best sword, upgraded items, great spin). It is posible that he is another Link who is still around while the current Link is in the middle of a quest.