Whenever I replay OOT I never have a problem with Navi. She rarely hard interrupts, usually just a short tone and flashing C button that goes away after a few seconds. The voice lines only trigger if you press the button to call her, in most cases the hints she gives are genuinely helpful, and stays out of your way for the vast majority of the game.

Fi from skyward sword though..... Far worse because she does interrupt gameplay, often repeats what the last dialogue box just fucking told you, and takes several dialogue boxes to tell you what Navi would have taken one to do. I'm glad they significantly overhauled her interactions in the HD release but I'm still going to be hesitant to play that game again