If anything, in future updates I'd say shipping should be made even more important and even more vulnerable. Because Aurora uses a jumpgate system, trade/shipping is by default quite safe. In the current system, if you want to put together a task force specifically for trade interdiction you need to sneak them through jump point pickets, which is a real nightmare unless you seriously out-tech your opponent or they don't know how to properly monitor jump points. As most intelligent opponents will have pickets monitoring their most critical systems, the only cargo/transport/fuel ships you're ever likely to catch are the unimportant ones going to out-of-the-way locations.
Don't get me wrong, the logistics game in Aurora is pretty damn fun. Still, it really could use some tweaking. More critical trade goods would be a good introduction, imo. Like, if that mining colony doesn't get its food shipment, it's liable to start starving. That kind of thing. Introducing an alternative means of travel to jump points sounds good, too, although I'm not sure how doable it is. There are several games out these days that offer multiple means of FTL travel (gates, warp drives, wormhole generation, etc.) That ship may have already sailed for Aurora, though.