2) Doesn't the shuttle bay have kind of a strange shape and position? A rotating, one deck thick donut right beside the engines. There would never be enough space to put even one light shuttle in there and docking would be a very delicate manoeuvre.
Actually it's in a good place. Remember, that part of the rotating section is the "outer deck", so the shuttles can launch with help from the ships rotation, just like B5's Starfuries. Docking would require some kind of "corkscrew motion", true, but nothing an autopilot couldn't handle (especially consoidering that a liner will use it's shuttles only under ideal conditions - stationkeeping near its PoD or Destination-, unlike a warship).