I really only see, Governments (Command Circuits), Armed Forces (Flanking), Pirates/Smugglers (Cattle Raids), Archeologists, using abandoned systems. Mostly for security reasons, or to recover some left over loot from when the world was inhabited.
An independent Merchant, would be looking at Cash Flow, unless he was wanted in 9 systems there is no reason to jump into uninhabited systems, by jumping into populated systems you always have the opportunity to make a few C-bills, Passengers, small compact expensive cargo, rare foods, booze, if you are jumping in with an empty collar, maybe even a fare.
Short of a National Emergency where time is of the essence and the government is dragooning jumpships, like trying to evacuate a world, or provide food stuffs to millions due to some manner of disaster, there is really no reason to jump into abandoned systems at all.
Smugglers/Pirates would want to use them, because there is a 30LY range for Jumpships, and only a finite number of populated wolds in range. If you are really wanted, your picture is going up on every law enforcement officers desk within 2 jumps of your last crime, with a Description of your Ship. Dead System jumping or Void Jumping is really your only option.
Armed Forces, people are going to notice a military flotilla coming through the system, your enemies spies will report it. Dead systems contain no spies, and if you happen to have one on your ship or command staff, it becomes a lot easier to flush them out with misinformation, like false jump coordinates. If you only tell 3 people what the false coordinates are and you jump into a dead system with an enemy fleet at the false coordinates, you only have to work over a small number of folks to fix the leak. By using abandoned/unihabited systems, your enemy know that you left, but they have no idea where you are going.
Archeologists, love dead worlds, especially from the Star League Hegemony Era, granted by 3090 most everyone of them has been picked over looking for WOB, but a few diamonds in the rough might still exist. Certainly the disposition of every Castle Brian isn't known, and there are enough old dad hegemony worlds, like New Dallas, which might contain something interesting and or valuable.
Command Circuits, just like the Kessel Run, straightest line is quickest, straightest line may not go through any inhabited systems, and a government will have sent ships, so they will know if they don't return and a rescue mission doesn't take 20 decades of jumping to dead worlds along the route.