^^ I honestly never found her annoying. It is easy enough to ignore her if you want to. The only slight annoyance was that first-person view was the same button, so if navi wanted attention, you needed to listen to her before being able to use first-person view. Still, that is so minor as to be meaningless.
This just perfectly expresses that special mix of irritation and love that we all feel for Navi. So many people get so worked up in taking sides of the pro/anti Navi argument that they lose site of what she really was--a helpful but annoying guide that lead many of us along our first path as the Hero of Hyrule.