Perhaps they use very small hyperspace openings that are either permanently open, or opened for fractions of a second each time they need to transmit something. The transmission itself might still be radio waves. Maybe permanent point to point openings allow longer range than ship based hyperdrives, and since radio waves have no mass they would have infinite range, therefore travel time might be effectively instantaneous within a finite length hyperspace connection.
That's my five minutes of thought on the subject, based mainly on how communication worked in the Commonwealth novels by Peter Hamilton and considering how I understand hyperspace works in Frontier. In Elite hyperspace was almost instantaneous anyway so perhaps communication just used small hyperspace openings.
