One is tempted to think that they don't radiate the excess energy - they transport it out, by implementing it into their assorted matter exhausts such as impulse jets. That'd be vastly more efficient and stealthy, if they can work out the processes needed to transfer the heat into those jets.
As for Janeway's plight in "Demon", it sort of makes sense. If the ship uses deuterium in all the ways the assorted Tech Manuals suggest, including fusion fuel, matter component in annihilation, and perhaps also propulsive mass, she's bound to be more critically dependent on deuterium replenishments than on antimatter rep. Also, if the ship indeed possesses the TM-indicated gadgetry for flipping part of the matter into antimatter, at lower than E=mcc energy costs, then replenishment of antimatter almost becomes a non-issue.
However, in order to work efficiently, this complex machinery probably needs deuterium specifically, and not just any random fusion fuel or hydrogen mix. The ship might run her impulse engines on all sorts of fuel, but in order to run all the different systems on the same fuel, she has to standardize on pure deuterium. And that's not all that easily found in nature. Refining/enriching it is trivial work, but requires a steady supply of both hydrogen and energy, and thus isn't ideally done aboard a starship that moves around all sorts of nonoptimal locations. If a starship is forced to transform herself into a deuterium refinery, this is no doubt best done next to a supply of already heavily enriched deuterium.
Janeway thus would never look for hydrogen. She'd concentrate on looking for sources of enriched deuterium - predominantly at friendly industrialized ports of call. And generally, she could count on a regular refill, since (as regularly pointed out) deuterium is abundant and easily enriched.
Yet Janeway would probably constantly be running well past the redline where the ship would have enough fuel left to hunt for more fuel from non-enriched sources. Indeed, the ship might not even have such a redline - it might be she could never convert enough natural hydrogen to her special brand of fuel to give the process a positive yield, not if grazing on normal gas planets or waterworlds, and least of all if grazing on interstellar gas. That'd never stop her ramscoops from gaining a little bit extra at all times - but this little extra would never amount to practical refueling. The equipment would largely be there for some completely different purpose, such as rapid back-blowing, or ingesting of navigational hazards, or other such applications.
It would make sense for Janeway to be running on fumes almost all the time on the hostile Delta Quadrant. Bigger and better starships have been suggested to have a fuel endurance of just three years. By the time of "Demon", that reserve would have been long gone, and probably the tiny but superfast ship never had that much reserve to begin with, being more a "greyhound" than a "husky".
Timo Saloniemi