Obviously ships can potentially run without a transponder. My suggestion there is make the engines of a ship register as an unknown transponder when active. Possibly even list the number of engines or size of them, but no name or other identification.
This makes it harder, but not impossible, for ships to run totally undetectable. It would also be fairly easy to make a large ship look like a small ship by limiting the number of engines running.
Also adds the possibility of a stealth engine type to be introduced, one that doesn't get detected, but is much slower than conventional engines.
Alternatively, add a way to 'run dark' with normal engines that dramatically increases the heat output that the ship needs to handle.
Idea being that the heat is easily detected, but if the heat is dumped into the ship rather than space, it hides the ship on sensors, but with the risk of overheating the ship.
This makes it harder, but not impossible, for ships to run totally undetectable. It would also be fairly easy to make a large ship look like a small ship by limiting the number of engines running.
Also adds the possibility of a stealth engine type to be introduced, one that doesn't get detected, but is much slower than conventional engines.
Alternatively, add a way to 'run dark' with normal engines that dramatically increases the heat output that the ship needs to handle.
Idea being that the heat is easily detected, but if the heat is dumped into the ship rather than space, it hides the ship on sensors, but with the risk of overheating the ship.