A powerful Rogue Trader dynasty might not need to defend his assets directly, but leave that to local governors and planetary rulers. For example a Rogue Trader may have set up a mining operation on a world which is controlled by its own governor (Imperial or not). The Rogue Trader gives a percentage of the opre to the governor and exports the rest of it. The world has adequate defences but no navy. The Rogue Trader can even supply a company or too of mercs for the governor.
Now if the world is attacked by xenos pirates (etc) then the governor can defend the world himself. If the governor decides to annex the mining operation then he won't have the navy to export the ore.
In short directly defending assets is potentially a problem only for those Rogue Traders who insist on complete control over a territory.
This isn't to say that a Rogue Trader won't defend his assets but simply that for most dynasties the fleet is the most important asset and as such I would imagine most dynasties would concentrate most of their vessels together, while having a few more wide ranging trading ventures.