They fit in with the overall atmosphere of the temple, imo. As for what connection they have to the "forest" element, I haven't a clue.
EDIT: Now that I think about it, I have an explanation. "Forest" is supposed to be like life. Trees, grass, other plants, they all come from the forest. In addition to that, the forest in this game could also represent innocence, Link grew up there and the Kokiri are forever children and forever naive. The poes, as ghost, are the exact opposite of this, they are the bane of life. Going through death, they wouldn't be all that innocent either. The Forest Temple was all out of whack, like Saria said. Having poes wandering about the Temple and screwing around with Link demonstrates this.
Of course, that could just be me thinking too hard.