Unlike English, Ancient (e.g. Attic) Greek does not reorder words to formulate a question. The particle "ἆρα" does modify a statement into a question, but is not always present. In that case, I presume there would have been a way for native speakers to hear the difference, perhaps in a change in overall intonation.
What device did spoken Ancient Greek employ to signal a question when the particle ἆρα was not used?
Since there are no native speakers of Ancient Greek around, I imagine having a definite answer to this question is impossible. In that case I would be happy with an educated guess, or a pointer towards current scholarly debate.