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Blood test or wait and see if apparently healthy birds suddenly become sick. Most carrier disease do not transmit through the egg, but a few do, Lymphoid Leukosis to name one.
If you introduce any new birds into a carrier flock, they will either become sick or carriers too.
I once had the pleasure of purchasing a bird from a breeder. It got sick shortly after I brought it home and it turns out that it had an UNKNOWN disease (as in it's never been encountered before!). Fortunately I did isolate the bird so the mystery illness could not enter my flock. But what a...