...in the next re-release/remake of Ocarina of time. /joking
Inspired by a theory on why Navi left.
As for why Navi is talking to TP Link at the end, remember how there is a fairy cursor that greatly resembles Navi in the game? It doesn't play a role in the story and never interacts with Link, but there could be another theory on why that is : P. Maybe it's Navi but, being a cursor, she can't contact Link...no matter how badly she wants to. Or it's simply a cursor (albeit a reference to Navi).
Just tryin' out something new!