I really didn't find her annoying. Her "Hey!"s and "Listen!"s I found amusing, and she's probably my favourite of the fairy sidekicks. I especially like how she follows you around, and how you can store and call her. I really thought she was a great addition to the series.
I suppose a lot of people's beefs with her are escalated based on the amount of times they have played through OoT. It seems the more they play it, the more annoying she becomes since she retreads information that's mainly essential to first-time players.
I have only played OoT once the entire way through. I have begun another file awhile back, and I've played through later parts of the game on friends' games, but otherwise, I've only done it the once. And even with starting a new file, it was many years after I completed the first file. Because of this, she never seemed to be repeating herself, or became annoying in stopping me when she wanted me to pay attention to something or where I should be going.
I know a lot of the game, but I don't know it like the back of my hand. So, I still need her to an extent as a "first time player". Therefore, I suppose she really hasn't had the time to get on my nerves.
I suppose my only annoyance with her is how she began the tradition of fairy sidekicks. I found every time there was a fairy sidekick I felt a bit gypped. I know other fairies had better character-based stories behind them, but I always found to an extent that it seemed the developers couldn't come up with a new design. Finally, someone came along and said "Let's just make them another fairy." So, my annoyance is that Navi started a trend of lazy sidekick visual designs, but even then, it's a small annoyance.