This is one aspect of Mass Effect's lore that I particularly enjoyed. They took heat into account when building the the Normandy - a stealth frigate.

It's a "stealth" ship because of two major things. Its hull's ability to deflect or absorb radar waves, and its heating/cooling exchange which was built in such a way that it can absorb heat into internal heat sinks for a limited amount of time, while cooling the exterior and engine emissions in order to reduce IR emissions.

With the stealth systems functional, you would have to find it by sight, which is hard to do.

They even discussed how the simplest way to disable many civilian craft was to disable their external emissive heat exchangers, since without them you couldn't run your engines for fear of cooking everyone inside. Warships had "tiger stripes" to limit the effect of losing one emissive surface would have on the ship's effectiveness. They also had methods of dumping massive loads of heat by ejecting molten salt (with an magic^w magnetic field collecting the cooled salt near the tail of the craft).