So their DPS could end up being very close. one just uses more arrows.
It makes sense of a physics stand point as well. To make an arrow go farther your going to need a longer draw(hence the long bow). By doing this you loading more power up against that arrow. When released that arrow is going to leave the bow faster and with more energy. So it will go father and will carry more energy and make a bigger impact when it hits something.
I'm pretty sure Longbows and short bows can use different length of arrows also, which would also increase the damage for a long bow as the arrow has more mass. However I've never seen them have 2 different arrow type for bows as that would be a little excessive and from a gameplay standpoint, one arrow is fine.