Can you not tell out of context if this sentence means The prisoners have not been found yet or Three prisoners have been found?
In this particular sentence, there is no way to distinguish. Context would probably make it clear, but both sentences would be said exactly the same in Klingon.
Is wej also used in the context of 'in spite of' as in 'Qang is stupid, yet he is the chancellor.'?
No. Never. For that, I would probably just use 'ach.