My, sort of in-lore, explanation for Nav Beacons is that they were originally intended to scan ships coming into a system to check for warrants etc and then transmit that data to authorities. They would also update any ships navigation systems with updates to the astronomical situation in the system, and/or changes to minor power alignment of stations/outposts etc.
However, after a time the Nav Beacons became an easily locate-able place for grey area / straight up illegal trades to take place. Due to the shady nature of the deals going down here, this ended up drawing the attention of pirates. Hence them being a good place to initially go hunting for them.
With the idea of them transmitting data on ships to the authorities, this would also play into the idea that a compromised one therefore wouldn't transmit infractions to the authorities, and therefore not calling in the security ships.