I wasn't personally annoyed by her saying "hey," "listen," and "watch out!" like others were. The only thing I really found annoying about her was when she decided to tell you where to go next every so often. It irked me the most when I was doing some optional thing, or when I was ALREADY GOING...
I really liked Navi, but I find it unlikely that they'd use her again. Though it is possible that we may see a very similar character in a future game.