People saying Frontier is lazy or doesn't think of things, I'm pretty sure that they thought of all of this.
It looks like they carefully considered the distance, locating it in a spot that it would have been able to get to in the time allowed, with some kind of conventional antimatter engines or maybe nuclear powered with improved technology.
They may have intentionally picked an inhabited system for entirely practical reasons. People need somewhere to drop something, and the system not being anarchy means that gankers at least have notoriety for what they do, and bounty hunters can get payout for it.
Back to the lore, I don't think it's far-fetched that a ship with a 2100s power plant would be missed especially if it was trying to be missed. Upaniklis is discovered. How many times do discovered systems get swept with the FSS/radio telescopes on stations/whatever? Even if we assume that stations' scanning capabilities are beyond those of the ADS or even the new FSS, is it reasonable to assume that the station would detect the ship automatically? If it can't detect it automatically, is it reasonable to assume it is actively scanning the system? And when UC is paying ships to do that anyway? And since UC controls the data trade, any scanning equipment the station has would be influenced by that, meaning the capabilities delta between ships and stations just got a lot smaller if the station's own data is being fed into UC's systems. If the station has its own scientific survey equipment that goes beyond UC ship spec, what is the point of using it? How often would it be used?
I mean think of this, most people have a home system or a couple home systems. Do you scan them every time you find yourself in them? Besides all that, the top speed of this ship, going by the distance we found it at 1200 or so years later, if it spent that whole time at top speed, which it probably hasn't, in a straight line to its current destination, which it hasn't, would be 150~ million kph. It would take these guys less than a day and half at top speed to go from the Sun to Pluto, or less than an hour to go from the Sun to Earth.
They could have made for the first system with a broadcasting listening post/transceiver of some kind. Or, because of some other reason, like needing a bunch of cargo canisters to make a giant circle for the hell portal, or something like that.