I would assume that there are plenty of uninhabited systems that serve as shipping lanes, so using those doesn't have the risk factor of going off into the Deep Periphery alone. If your helium seals blew on a shipping lane, there'd be other ships along before too long to help out.
Notably, when the GDL leaves Galatea in Mercenary's Star, their first stop is an unmapped, presumably uninhabited system.
If you look at the 3025 map, Dixie is a Lyran world, but is more than 30 LY from any other Lyran world. If only inhabited systems were allowed to be used, the Lyrans would have to get in and out of Dixie through FWL space.
Of course, the existence of uninhabited systems for transit breaks some of the plot points from early books, which talk about various sides blockading systems by occupying the zenith and nadir points at inhabited systems between them and friendly systems. If you can just go through uninhabited star systems, those blockades are utterly pointless. (Likewise Janos Marik's order to "blockade the border" with the LC to prevent Snord's Irregulars from getting back into Lyran space with their recovered booty.)