It's a tricky one, you know. Each person will have to do what's right for their farm and their chooks.
For me, I don't buy hatchery chicks or chickens very often. Most years, we hatch our own eggs. For our home hatched hens I figure that I'm very careful about not introducing new birds to the flock and if someone gets sick or dies, I make sure I know why. Even if that means sending the bird to the lab for tests. I monitor the health of the flock daily.
My theory is that in a commercial hatchery there are a lot of chickens. Often living inside. I don't know the ventilation conditions or the hygiene requirements they have for their humans. It seems to me, if someone is careless, that's the place the chicken is going to pick something up. So when buying from a commercial outfit, I go with the vaccine option. When home hatched, I don't.
We have had illnesses go through the flock and one year we lost half our hens. But this was a monoculture breed that we got as day olds from the big hatchery. We culled the rest of the flock that winter and got a mixed heritage large brown egg layer from Murry Mac Murry (or whatever their name is, I haven't seen it written down). Lots of genetic varation. Very illness reistant. We might bring in a new cock every 5 years or so, but the result of the decendants is a vibrant barnyard mix that has had very low casualty rates.