I don't think anyone really "knows", I've heard or read a number of explanations, from the fences enclosing standing fans at field level being called bullpens (then that bit of ground being surrendered to the pitchers) to the Bull Durham ads. It could be as simple as where one keeps a collection of studs.
On Deck, In the Hole, K, Annies....baseballs taken their terminology from n interesting and broad range of sources. Bless those colorful writers!