The reason people profess to find Navi annoying the vast majority of the time is because that's what everyone seems to say, and conclude (if subconsciously) that this is how they are supposed to feel about her as well.
I choose not to agree with that sentiment. I loved Navi. Her saying "hey," "look," and especially some of the rare ones like "what's up," if anything certainly weren't annoying. It gave her personality. I also loved seeing her fly in and out of Link's hat and around his head, which you never hear people complaining about. People complain about her voice acting, which is, in truth, delightful, but not about the visual aspect of her character. It's a nice touch to the ambiance of the game world.
People fall into popular opinion and tend to fail to realize that she's more than just a fluttering avatar. She's a real character in the story with her own personality and role, and that role certainly isn't to annoy Link. This kid grows up in the Kokiri Forest, bullied because he's the only kid there who doesn't have a fairy, then one day Navi comes to him. I can't imagine under the circumstances that he would be quick to be annoyed by his new fairy companion. If anything, he should be ecstatic to finally have a fairy of his own, so there certainly has to be a great degree of companionship between Link and Navi, although it's an element of the story that should come largely through the player's imagination of his or her hero's character. There's a certain sentimentality to
, and it's not an unpopular theory that Navi is the one for whom Link is searching at the beginning of
Majora's Mask. If Navi was a pest to him the whole time, why on earth would he go looking for her?
I will admit that some of her slow, unskippable text bosses were a bit annoying, but those only appeared two or three times inside the Deku Tree, and to a new player they would likely be helpful if anything. It was ultimately a minor twitch, however, and nothing really detrimental to Navi's character. I appreciated at least that the 3DS version of the game made these text boxes more effectively skippable, rather than requiring the player to wait for it to fill up.
Overall, though, Navi was never a nuisance. She was a pivotal character to the plot, and a delight to have along for the adventure.