Again, I think you're reading way too much into it (why doesn't anybody read my posts?). Bosch only figured out the technology that the Shivans use to communicate through large distances or through a vacuum. Humans do this using radio waves, but that doesn't mean we evolved to have radio transcievers integrated into our skulls somewhere. Instead we use a technology we call radios to convert sound waves into radio waves, and then convert those radio waves back into sound waves that we can understand. The ETAK project was a study in Shivan technology, not Shivan biology. Bosch learned the technology the Shivans ships use to relay messages to one another, not the way two shivans, standing next to eachother in their natural environment, would talk to eachother.
We have no idea whether the Shivans understood wtf Bosch said, or if Bosch himself understood wtf the Shivans were saying, but he probably piqued their interest because he found out how Shivans relay messages from one ship to another. Maybe they were interested because no one had ever interfered with their communications before, or maybe because they wanted to kill him before the GTVA could adapt the technology and use it to decipher what the messages between their ships mean, thusly giving GTVA a tactical advantage in combat, or maybe, if the Shivans so have some sort of hive mind, the messages that Bosch was sending interfered with their ability to think, and wanted to shut him the f up as quickly as possible, and capture him to figure out how he "got inside their heads".
Edit: Bosch did use info from the defunct GTI project involving the study of live Shivan specimans, but we don't know how the "quantum pulses" are related to the way two Shivans might communicate normally. The quantum pulses are used by Shivan ships to transmit messages to one another, exactly what these messages sound like to "Shivan ears" once they are demodulated we don't know. They could communicate in the visible light spectrum, or with infra-red, or with something else. However, the quantum pulse part of the ETAK project is definately not how Shivans communicate conversationally, but how messages are transmitted over normal space amongst the Shivan fleet. Messages over subspace are probably transmitted via those "comm nodes" you see in "Into the Lion's Den," much like how the GTVA uses relay stations, in the form of GTSC Faustus installations.