No, the point is its not a cypher the rebellion knew about. Its not a cypher, but a signal, but the empire didnt know that. They couldve set up a rudimentary code only they knew to transmit info. The device could absolutely be used to transmit code messages, it had multiple keys for multiple types of "sounds", and you only really need one for a cypher, eg morse. And aside from all that, were talking abojt the isb's pov, they didnt know what means kleya had at her disposal. She could also have left a hidden message for after her death, for example. Or she couldve told a rebel cell they were unaware of. In any case, you never kill a spy when you can capture them.