Most of the scoring rules in Agricola makes sense because they reward you for doing well in various categories (like crops and animals). However, I haven't been able to figure out why the rules reward fenced stables with a bonus point. When combined with the fact unfenced stables can can only hold one animal, this seems like to make unfenced stables unnecessarily weak. Why did the game creators choose to add an extra point for fenced stables?
Unfenced stables give you a point by removing an unused farmyard space at the end of the game.
Since you get -1 point for each unused farmyard space, and stables count as a used farmyard space, they are also 'rewarded' with one point. In order to keep the balance, the rules ensure that you effectively get one point for each stable no matter where it is placed. This allows stable placement to be determined solely by your desired animal capacity instead of points for the stables themselves.
Alternatively, the game creators could have removed both of these benefits and given stables no points, but that would have made stables far too weak in the game.