I have discussed about the hanger with Raxar and my hanger sinks into the hull slightly.
Here is the thing - I made that assumption when I measured the heights. The 14 foot height assumes that the gun gallery is on the same level as the hanger, and the 12 foot height assumes that the deck is generally level and is above the top level of the aft portholes. Even if the aft level of portholes are on the same level as the hanger deck level, you've got at most 18 feet (which would be enough for two decks), but you've still got the deck height issue aft, and you've got a gallery area that doesn't match up with any deck. This would cause stress and problems, not to mention difficulty in access.
And the flight deck does not take any hull stress it is thick to try and stop bombs from reaching the soft nether-regions.
Congratulations, you've introduced a top-weight problem. If we assume you've got a deck of STS (Special Treatment Steel), you've got a thickness of 24 inches. In all likelihood, it's more like 5 with a 5 inch cover of wood and the structural supports bring it up to the 24 inch thickness we see. Even with just 5 inches of STS, each square foot will weight 200 lbs. That's just for the armor. That's on par with the deck armor of BB-49, which didn't have the disadvantage of having to support the armor over a large empty hanger. I strongly recommend that you find a resource and read up on aircraft carrier design before you continue.
For an example of why this isn't the best idea, take four sheets of paper, and wrap them around a soda can. Tape them up so they are all the same height and diameter. Now place them upright on a table, and put a hardcover book (something substantive, such as a text book) on top of them.
Now shake the table.
Even if you tape the book to the paper, and the paper to the table, it's going to sway, and probably fall over. This is a semi-practical example of why this is a Bad Idea™. Putting the armor under the hanger deck means that you don't have to have a big hole in it for the elevator, and you don't have the weight up so high. Also keep in mind that the Essex class, the first carrier to start carrying armor protection above the hanger only had 1.5 inches of it. While the British did use armored flight decks, I don't have direct access to the specifications thereof. The reason the US didn't was because a thinner deck would be easier to repair when damaged as well as not overly contributing to the top weight of the ship.