With a propulsion system as powerful as the Epstein Drive, any spaceship is a potential weapon of mass destruction if it crashes into an inhabited body or station at high enough velocity. A single drunk driver could kill thousands, if not millions. So I'd expect every such spacecraft in the system to be carefully tracked as a routine precaution.
That's also covered in the novels: it's the whole reason ships are required to keep their transponders on, so traffic controllers can know where they are. If you turn off your transponder and "run dark" you can go undetected as long as you're in deep space and far from any legitimate ports. But once you get into the airspace of, say, Ceres Station or Vesta, running with your transponder off gives you away as either a pirate or fugitive and in any case they'll burry you up to your eyeballs in fines as soon as they spot you. You can't dock at a legitimate port with your transponder off and you can't do commerce with anyone who finds out you've been doing it.
On the other hand, space is still very, very BIG. A space ship flying teakettle (that is, without its drives and using only the superheated steam in its maneuvering jets) doesn't stand out against background radiation from any significant distance, and even if you just happen to detect it, it's hard to tell it apart from random space debris, uncharted asteroids (of which there are literally millions) or a false positive. IOW, if a ship doesn't want to be tracked, there are all kinds of ways it can make that happen, but as soon as it tries to DO anything more interesting than drift and float, it'll show up on security scans across half the solar system.
Besides, it was coming from Ganymede to Tycho Station. It would be known where they were in their orbits at the time, and it would be known roughly when it launched and when it arrived. And the laws of physics are a constant. Given that information, there's only a narrow range of trajectories the ship could've followed, so it wouldn't be that hard to determine where to look in the sensor records.
True, but it WOULD be pretty damn hard to visually confirm a cloud of bodies floating away from the ship. Even if you pointed the Hubble telescope DIRECTLY AT the ship at the exact moment it was dumping the bodies, its angular diameter in Hubble's field of vision would be a couple of pixels at most. So what you would actually see is:
Big bright dot gets really small (can barely see it).
Stays small for 60 seconds
Becomes big bright dot again.
All the captain of the ship would have to say is "Ima lowda choked on his kilbble and we cut drift to space the body. See? It's right there in the nav logs, sa sa que?"
Even aside from that, there are lots of people with telescopes. A lot of bad sci-fi postulates the government keeping events in outer space secret from the public, but that's nonsense because there are countless amateur and professional astronomers constantly watching the skies, so things in space are hard to hide.
Yes, but things in space are also hard to SEE. I can point my 8 inch reflector at Jupiter right now and see all four of the Gallilean moons, but if you asked me to find 101955 Bennu, even if I knew exactly where to look, you're basically asking me to find a black dot on a slightly blacker background.
Anything smaller than, say, the moon is only going to really show up with a long-exposure image.