Using ozone to clean fruit and veggies is a surface clean.
Unless the produce is particularly porous, I don't think it
would get inside to destroy any of the nurtients.
As for the good bacteria, there are a couple of different
types of good flora in the intestines: aerobic and anaerobic.
The aerobic bacteria will be fine in the presence of ozone.
They'll quite enjoy it. The good anaerobic gut flora has a
different cell structure than the bad anaerobic bacteria
such that they are considered "facultative anaerobes", which
basically means that they can live in the presence OR absense
of oxygen. The only thing I am unclear about is whether or not
ozone will kill facultative anaerobes. I would think not, since
they can live in the presence of oxygen, and ozone is in a sense
a form of oxygen.