i don't vaccinate, but it's a personal choice. we're organic and, while we could vaccinate when they are day olds and still be organic, it's not worth it for us. it really comes down to how you feel about it.
vaccinating is probably going to save you time and money to a certain extent. you won't have to be quite as vigilant about cleaning, etc. you will probably loose fewer birds in the long term.
but i've also read that vaccinations are responsible for the majority of chick deaths because their immune systems are temporarily suppressed by the vaccine, which makes them susceptible to a lot of other things. so you open the door to one thing by preventing another. but again, it might be better to loose chicks than it is to loose birds you've put money (and feed) into.
vaccinating for cocci isn't necessary if you take other measures. the problem with cocci and chicks is that the bacteria builds up in the digestive systems too fast for them to handle. keeping the brooder clean and giving them lots of good bacteria should mostly eliminate any cocci problems. supposedly raw goats milk is a great preventative for cocci. live yogurt cultures should help too. but the important thing is to CLEAN! it obviously doesn't need to be spotless, but a little fresh bedding every day and a good clean every week go a really long way.
as for Marek's, once you vaccinate for Marek's you always have to vaccinate. you run the risk of introducing the virus into your soil when it's not actually there at all. however, birds can be carriers and show no symptoms, so not vaccinating means you have to be really careful about what birds you bring into your flock. Marek's is bad, like wiping out half your flock bad, but you have to weigh the possibility of infection against what the vaccine does to your birds.
only day old chicks can be vaccinated for Marek's (as far as i know), so if your chicks haven't gotten it then they are past the window of opportunity. if they came from a hatchery, especially through a feed store, then they probably got vaccinated.
good luck with your chicks!