, regarding the deck below the hangar, I might suggest simply having that section/room have a 'stepdown' from the rest of the deck to allow a safer clearance for the shuttles.
Also, I don't think we've ever reached concensus on the number of shuttles. Common sense would suggest seven based on the '7' on Galileo
, but for all we know there are only two Class Fs (Columbus
, and of course then the replacement Galileo-II
) and everything else is a different type - among them, inspection pods inspired by Jefferies's unused drawings perhaps?
If we assume that the ship didn't have any landing-capable shuttles in 'The Enemy Within' we might then conclude that the embarked craft load changes frequently and there is no 'standard' set.