there are a few respitory diseases that can be carried in eggs from what I have heard (MS, Corza,MG) google those. I wouldn't say that hatchery birds are disease free but if they did have a disease, that hatchery wouldn't be in business very long.
IC is NOT transovarian. It is a direct contact only. MG IS transovarian. It is also the one that is often the silent threat as it has asymptomatic carriers. Hatcheries do often immunize as well and you should know that by mixing your hatchery birds with your breeder birds who are typically not immunized the hatchery birds can slough off disease to the breeders. It is a small risk but a risk that I learned existed. Additionally, MS is not a respiratory disease. It presents as a joint disease whereby the bird is seen to flounder as it tries to walk and eventually can not walk at all.
This is an easy to read site about poultry diseases but I recommend reading the one I linked earlier about MG because once you know what to look for you can avoid trouble.
http://www.merckmanuals.com/vet/pou...overview_of_infectious_coryza_in_poultry.html
I remember going to this man's house looking at his birds-- I was there for geese, but given how he kept them I was ready to leave without anything. Then I saw my first spangled Hamburg. This was last year. I remarked then on how small they were. Well, I bring this up because this bird had very strange looking legs. NOW I know why. At the time the man pointed at them and said it was because the chicken was old. Nope. I have seen old chickens without this issue. What I was seeing then and thankfully avoided having here was leg mites!! When I went to a very nice breeder, a person who also shows and does well AND has a beautiful farm, to look over his birds one of his birds had a head full of dirt. The "dirt" was lice and mites. I am going to sound bossy right now and I hope you will forgive me but: handle the birds you want to buy and look them over!! Look at the eye closely, the feet, under the wings and butt fluff. Are the birds clean? I am not saying spotless. Do you see little bugs? Do you see gleet or feces? Do you see scales missing or cracks in the pads of the feet? Are the eyes clear or do you see worms or bubbles or swelling? Feel the birds keel-- this is the breast bone. Is it sticking out?? Is there flesh to either side of it? Things happen. Birds pluck each other, birds mount each other, get into fights, birds get into mud and even poop on each other but those things are reasonable, though embarrassing to the seller. Learn the basics and save yourself some heart ache. Treat your chickens like the investment they are. I also learned that it is a reasonable to worm your birds when they arrive-- thank you Hoppy. Just live without eggs for another week or so... although I just read about something that is only a one day withdrawal. I'll try to find it. And quarantine should be for more than ten days if you really want to be sure of what you have. Simple enough steps can give you a good chance of having a happy flock.