A person might assert that it's most efficient if the equipment works with natural convection rather than opposing it: blow cold air downward; blow warm air upward. I believe this doesn't really matter. Ultimately the job of the blower is to overcome not only convection forces but also duct friction to push the conditioned air to where it is needed.
There are whole-system advantages when a space is cooled by blowing in air through registers in the ceiling, or when a space is heated by blowing in air through registers in the floor. Mainly this is due to the fact that good mixing naturally occurs between existing room air and newly-conditioned room air. Cold air delivered at the ceiling is going to naturally settle downward toward the floor, mixing with and cooling existing room air on its way, and similar happens with warm air delivered at the floor. We generally prefer our heads to be in cooler air and our toes to be in warmer air. We might be able to set the thermostat a degree or two warmer or cooler than normal as a result, and that's an efficiency gain.
Furnaces exist for upflow, downflow, and horizontal flow mostly for practical reasons having to do with the duct system. A system in an attic would often be positioned horizontally partly so the ductwork can lay on the attic floor, but also because many attics are not tall enough to fit HVAC equipment vertically. Whether the furnace is upflow or downflow doesn't matter when it's on its side!
In some buildings it makes more sense to put the ductwork in the floor; we use downflow furnaces to make that possible.
There is one big drawback to downflow furnaces: the burner is at the "bottom" of the furnace but exhaust gas has to go up. The exhaust of a non-condensing furnace needs to rise; the liquid condensate of a condensing furnace needs to drain/fall back toward the furnace. In either case the flue has to pass in front of the blower, which makes future maintenance of the blower a little more difficult.