AFAIK, you can't store heat under thrust. That's why you'd void the heat sinks at that time.
Think of it like a submarine. There are many things they can mask, but sounds can only be dampened to a certain point. And while the most modern subs are incredibly quiet when moving, they're not undetectably so. The stealthiest propellers still make noise. So one of submariners' tactics to maintain stealth is immobility.
Likewise, a stealth spacecraft would only use thrusters when absolutely necessary. With good heat sinks, and insulation, such a ship not under power might be virtually indistinguishable from debris or meteoroids.
