There are 3 possible results after infection with a communicable (contageous) disease:
1 death
2 infection, symptomatic or not, leading to chronic infection and a carrier state
Typical diseases that this is seen with include herpesviruses (chicken pox, cold sores, Mareks disease), typhiod (think Typhoid Mary), and chicken diseases such as MS and MG.
3 Infection, symptomatic or not, which the birds immune system resolves, leaving a healthy bird without carrier state.
The number 3 birds are the ones we want to perpetuate. They are the ones with a healthy immune system and an ability to fight off infections.
Unfortunately, 2 and 3 can only be differentiated by testing, such as throat swabs or blood tests. This could get expensive if testing multiple birds.
My personal opinion is that if you know your flock has a disease in the number 2 catagory, your flock should be closed to outgoing birds, and you should seriously consider if you want to add birds to an infected flock.
A far as vaccination, it can reduce clinical disease incidence (meaning actual signs of illness), but not necessarily infection. vaccine success depends on several things, starting with selection of pathogen strain, proper handling and administration, to the adequacy of the immune system response to the vaccine. Should you vaccinate? Absolutely if your birds are at risk of exposure to an infection. But, keep in mind that vaccines are not 100% effective, and are intended as a population tool, not for complete protection of every individual. So vaccination will be more effective if all the young birds are vaccinated.
Sorry if this is a little technical!