This is what I like about Naomi:
She's smart but she's no girl genius. She never saves the ship, nor is she a catalyst for Our Heroes to have tedious epiphanies. She's just an intelligent child, into her academics and wanting the respect of the Captain and 7. She has no peers as she is the only child until the Borg kids show up so her interactions with crew are not some weird child-prodigy hanging out with adults deal. They are they only people she has to talk to.
She's not particularly emotional, you can see she would have been the geeky girl back on Earth that looked down on the cheerleaders. But there are no cheerleaders here on Voyager, she's got no one to feel superior to. At no point does she come across as snotty or know it all. Her life is not idyllic however.. though she is cared for and encouraged by any in the crew she interacts with she still has reason to fear those that would do Voyager harm. She has had to grow up quickly to realistically understand Voyager's vulnerability in the Delta Quadrant.
There's not a single moment she annoys me. She's utterly normal given her unusual life.