While the ship could be presumed to have some baseline thermal load due to running equipment, we can consider it to be extremely low compared to the heat generated by the engines moving the craft at hundreds or thousands of kilometers per second. Your 'thermal signature' likely would not even be based on the average temperature of the vessel or even it's engines, but would be based on something analogous to an exhaust temperature. Parts of the exhaust would consist of hot, ionized plasma (from the thorium fuel you are burning) which would strongly radiate in the infrared, possibly even the visible or ultraviolet. When your engine isn't running, you are now a somewhat warmer rock than natural rocks in your neighborhood, but couldn't hold a figurative candle to your engine output.
While we can detect rocks, etc, with visible or IR telescopes, such detection takes much longer and we can argue for simplicity's (gameplay) sake that such sensors would have to be much more sensitive and would not be practical for shipboard use. Current sensors also look at an extremely small portion of the visible sky at any given time as well.
Mike
