I certainly sympathize with those who loose their birds. A good friend of mine lost his entire beef herd to tuberculosis eradication several years ago, and it was a great loss in both a material and emotional sense. It might help to understand the process if you know how testing works.
There are two kinds of tests available for diseases.
Antibody test - antibodies are produced by the body in response to exposure to infectious organisms. A positive antibody titer test means the subject was exposed to infection with that particular organism and developed an immune response, but not if an active infection is present. It can be used to monitor if diseases are present in an area. After vaccination an antibody test will tell you if you have developed immune protection to the infection vaccinated for. There is no way to tell the difference between antibodies produced by natural infection or those due to vaccination.
Because it takes time for antibodies to appear, animals can be infected and not test positive for a while, sometimes for as long as months. That is one reason why diseased such as HIV and tuberculosis can be so hard to detect early.
If there is a chance that birds were exposed to an infection that may have a long latent period, then the decision may be make to kill them, as quarantine is often extremely expensive and could not be done in most cases on a home farm. I mean no disrespect to anyone, but people can be very undependable when it comes to strictly adhering to isolation, and quarantine for some diseases may be months long. In addition all waste products such as bedding and manure, and even the dust in the coop, would have to be treated as a biohazard.
Antigen test - this tests for proteins produced by the actual organism itself, and is an indication of an infection, whether the animal appears sick or not. There are, unfortunately, not many infections that can be tested for in this way due to complications regarding how organisms act in the body.
