My free range chickens have been amazingly germ- and parasite-free. Despite all the wild birds. I think if they have access to full nutrition they are able to self-medicate and their immune systems are strong enough to fight off most problems. We got one once that had been in a small cage on someone's deck. She was missing lots of feathers and didn't seem too healthy (a rescue -someone had to get rid of a pet). She ate lots of artemesia (wormwood) and was the only one that ever ate it, then her feathers grew back and she was quite nice.
If you look them over when you get them, I wouldn't worry too much about germs, etc. The main issue is if it's a dishonest seller trying to pass off an old hen that quit laying instead of a new one. Just 1 year old or slightly younger is ideal - you should get two good years of eggs out of them.
Here's a pretty good checklist of how to tell if a chicken is healthy:
http://www.dummies.com/how-to/content/how-to-buy-healthy-adult-chickens.html
