Basically the way you would make a stealth spaceship would be by focusing as much as possible on energy efficiency. At every juncture you would try to use as little power as possible, and use every bit of it as efficiently as possible, so that you’re not remitting waste. That waste, in the form of heat, radio waves, etc, is what gets you spotted.

You could also run heatsinks temporarily for enhanced stealth as you suggest, then open up radiators to cool them - or eject them - once it’s safe to do so.

(For the Elite: Dangerous players, yes, that game got it right.)