Yes, but the transporter is a boon when you are constipated! --thebiggfrogg
Yes, they do, and this was an issue with which Zefram Cochrane confronted Geordi and at which Geordi at first feigned ignorance of, in Star Trek: First Contact.
If you want to get a great laugh while listening to a discussion on this topic, listen to the Star Trek: First Contact commentary by Damon Liendelof and Anthony Pascale. Don't worry, they don't spend the whole 2 hours talking about it!