Link and Navi - Note to Watchers

Link does not hate Navi.

I cannot begin to express how frustrating it is when i get questions like "Isn't Navi annoying?" and "Why haven't you killed Navi?"
Link will not kill Navi because she is his best friend in that lifetime.
Think about it, all those people he met? They could never imagine what Link is going through. He just got thrown seven years into the future where Hyrule is in ruin. He's a little kid who has to fight for his life and everyone else's. No one else other than Navi and Zelda could begin to understand that. Yet, when he finally reunites with Zelda, she sends him back in time. He's just lost that friend- and not only that, but when he returns to his time, Navi leaves. Link would be devastated.
Navi was with him for that entire journey, giving Link the outside information he would have never known being a sheltered Kokiri. Without Navi, Link could never have survived his task.

I don't think one too many "Hey Listens" is going to change how valuable Navi is to him.

Navi is his friend. His guardian fairy.
To a Kokiri, your fairy's part of you.
To Link, your fairy is the only one who knows that other part through and through.

Only Navi knows the future Link left behind, and i'm sure that's part of what motivated him to go searching for her in Majora's Mask. You try living in a world where your heroics never happened. No one knows what you've done for them.
No one but her.