As far as putting the packs in the space between the deck and the under brace - you will probably have to make the brace peice wider to create a larger space.
On my current version, the space is too smal for a TP 3S 1320 pack to fit all the way inside. You would have to leave any "hatch" off or build up a deeper pocket for the packs.
As far as cooling - the way I fly mine with the motor Im useing, my packs never get warm even in the summer. If I put my packs inside the pocket, I'll probably seal up the front for the same reason you mentioned.
In the winter it would probably help keep the packs warmer so you would actually get better performance on very cold days.
Be sure to leave the back end open so any water that does get inside can drain out.