Commercial operations can and do vaccinate against several things, but at the hatcheries we normally buy at, the two options are usually cocci and Marek's. You can do a search in either and get a lot of detailed info.
Cocci is caused by protazoa. The protazoa reproduce in the chicks digestive system and wet manure. If the numbers of the protazoa get too large, it can weaken or kill the chick. Medicated feed reduces (does not totally stop) the reproduction of the protazoa in the chicks intestines. If you keep your brooder, coop, and run fairly dry you usually do not have a problem with cocci. There is one very strong strain that can cause serious problems even with dry brooders. There are several different varieties of the cocci protazoa, seven I think but its been a while since I read up on it. The vaccination does not protect against all seven, just three or four. If you feed medicated feed or give them antibiotics the first two or three weeks after you get them, you nullify the effects of the vaccination. The chicks need to go through a few cycles of eating the protazoa eggs, letting them grow in their intestines, then eliminating them to eat the eggs again to develop immunity to that strain of protazoa. They best develop this immunity as very young chicks.
Once cocci is in your flock, it stays in your flock. If you have that nasty strain of cocci in your flock, then the vaccination is probably a good idea. I don't know that the nasty strain is one of the ones covered in the vaccination but I would hope so. I do not vaccinate for cocci. I keep my brooder fairly dry but allow damp manure to build up enough that some of the protazoa can live in it but not wet enough so that the numbers get out of hand. Their first grit at day 2 or 3 is slightly damp dirt from the run to introduce any cocci that is in my flock to the new chicks so they can develop the immunities they need to.
The Marek's vaccination is actually Turkey Marek's, not Chicken Marek's. It does not prevent Chicken Marek's but prevents the lesions that cause the damage. Chickens that have been vaccinated with Turkey Marek's can still get Chicken Marek's and can still give Chicken Marek's to other chickens. They just will not show the symptoms or damage themselves. Marek's is another thing that if it is in your flock, it stays in your flock. And some Marek's is more deadly or damaging than others.
I live in an area of high commercial poultry production. It's Tyson's headquarters. The University of Arkansas Ag Department does a lot of poultry research, mostly paid for by Tyson and other commercial operations. The local Extension Office (in the phone book under county government) is very familiar with chickens and their diseases. When I called the county extension office, the agent put me in touch with a professor at the U of A Ag Department that raises and breeds chickens, used to show chickens, and is very active in tracking local chicken disease outbreaks. After we discussed how I planned to manage my chickens (start with hatchery chicks, not show them or participate in chickens swaps or go out of my way to expose them to any other chickens, bring in new blood by hatching eggs or getting hatchery chicks not adult chickens, not allowing any of them to live past three years of age, etc) and discussed what diseases are in my area and how often they strike, I elected to not get the Marek's vaccination. I was lucky, thanks to all the emphasis on commercial operations in this area, to be able to find someone very knowlegable in my situation and with all the tracking and controlling of chicken diseases in this area to wind up in a place that is actually pretty safe to raise a hobby flock. I suggest you call your county extension agent and try to detemine what diseases are active in your area to help you decide on how to manage your flock from a biosecurity viewpoint.
Good luck!
