Jessica
My understanding of using ozone to deoderize books and other materials is that the treated books are entirely safe for people. The only concern is that this treatment will likely speed up the rate at which the organic material - paper, leather, etc. - decays.
This won't likely be a concern for things you anticipate aren't going to be on your shelves for longer than 20 years, but it is something to be aware of.
As far as I'm aware there are no real strong alternatives for removing smoke odor. There are other techniques which will likely involve more time and energy which, although they don't pose the challenges of ozone, yield mixed results.
Kevin