The head tubes are short to allow people to use aerobars. It's really difficult to get low into aerobars if your headtube is long.
So, it's more useful for a rider/racer to have a short head tube and use a rise stem that extends than have a long head tube and have a snub of a stem that is almost vertically downward.
EDIT:
Also, for aerobars on a tall head tube, one can't just use a downward stem. The stem lengths are much shorter when using aerobars
