When I started recording audiobooks I started hearing breaths in my work and I panicked. Should I leave them in or take them out? After studying a few of my favorite audiobooks I decided to leave some of the breaths in. Not all but most, because some breaths are not always a bad thing. Breaths can help communicate emotion or bridge one idea to another. That pause in a read is a dramatic statement. Listen the next time you turn on the radio or TV you'll hear inhales on many phrases and sometimes you won't. Often, a breath can be acceptable if it connects sentences into a flowing thought. I even convey the story with, a snort, a laugh, a hiss, a long breath, or even short breath because they all communicate the story to the listener.
But they can also be distracting, such as at the beginning of a paragraph or a long pause while you catch your breath. So, for starters make sure you are recording in a studio with good room acoustics so you can listen later to remove the unwanted breaths and keep the natural sound coming.
There are ways to set up your recording software like Audition to try to remove and keep breaths in but to be honest I have always liked the hands on approach when doing audiobooks. I just think it's important to in control of the sound you want, and I think you'll be happy with results.