As a disclaimer, I'd like to first state that I am not a vet--what I am about to say is based entirely on lots of my own research, and I would suggest that anyone reading this do their own research to make sure that what they end up doing is right for their flock.
I do not vaccinate for Marek's for one reason--I am fairly sure my hens that were feed store chicks were not vaccinated. It's my understanding that birds vaccinated against Marek's can also shed the virus and infect birds that are not vaccinated. Marek's is a nasty disease, and I don't like the thought of it getting into my flock, but I'd prefer not to bring it here myself and risk losing any of my birds. The vaccine is only really effective within the first 36 hours after hatching, anyway, or you can bet I'd be vaccinating my girls for it.
Whether it is worth it to have the hatchery vaccinate really depends upon which hatchery--and you'd have to be asking that hatchery about it. Apparently, not every vaccine is effective against all strains of Marek's, but some hatcheries reportedly mix the three vaccines to cover all strains. If it weren't for my situation of having some birds not vaccinated, I would likely vaccinate chicks if it was the mixture of vaccinations to cover all strains.
As far as contamination goes--this is exactly why I don't like to buy adult birds anymore. Any adult bird could potentially be a carrier of a disease that it does not show symptoms for. Additionally, any place that has adult birds, or that someone who owns adult birds has been (yes, this includes the feed store!) can be a source of contamination for your flock. There are lots of ugly diseases out there, and if you really want to be safe, you have to be proactive--never wear the same shoes or clothes in the chicken yard or where your chickens may be after you've worn them to a swap meet, someone else's farm, a poultry show, or even the feed store, and vice versa. Of course, there is now way of preventing all contamination, as wild birds and insects can carry some things as well, but you can always do what you can to help prevent your flock from getting sick.
As for medicated chick feed, I avoid that as well. The medication in it is just a low-dose medicine for coccidiosis to prevent your chicks from getting it, nothing more. The risk there is that if you bring successive generations of chicks in on medicated feed, the cocci on your property could become immune to the medicine in that particular starter feed and your birds could become infected anyway. I feed the unmedicated chick starter and keep some Amprolium on hand just in case the chicks come down with coccidiosis. However, if you really want to feed medicated starter, you could find out what kind of medicine is in each brand, and switch between brands that use different medicines each time you get chicks.
I feel the same way. I was upset the hatchery told me it was too late to vaccinate, and the 6 i bought from the feed store were also not vaccinated. I will not vaccinate any of my birds because this first set was not. I don't plan to visit any swap, and I do change shoes and clothes once I leave the feed store. I have no friends who have chickens. I kinda felt like I was going overboard. I am glad to see that I am not going overboard. It is serious and I need to treat it as so.
Thanks for the confirmation.
Deb