I do it occasionally, either for excessive dead air that kills the flow of the set (usually a case where I found the downtime annoying at the show itself), or if someone yells something really stupid, really loud, near the mics between songs, and the performer doesn't incorporate it into their own banter, I'll cut that. IMO whatever makes a recording more enjoyable to listen to is fair game.
The exception for me is if I know someone will need my audio for video, I'll leave it intact to save them grief in editing.