In StarGate Atlantis, McKey said, that there is a 50:50 probability that Atlantis will be ripped apart into pieces if they enter the hyperspace with reduced shield radius (they had a ZPM power shortage)
And now Imagine the distance between stars!
Maybe navigate within a planet orbit is a lot easier than cross the light-years in minutes or hours with FTL systems with a station not built for the forces of Wormholes / Hyperspace-entrances / etc.