So what you're saying is that this might not be the best design?
Yep, exactly a horrible design. Seriously.
If you want to put the flat top on top, you have to add much more mass below. If your imaginary world has something _other_ than Hydrogen or Helium in the gas bag, you might be able to make _that_ work.
Let's imagine that the bags are filled with refined æther (the mythical medium that permitted electromagnetic waves to propogate) and that when energised to create an anti-gravity effect it provided, say, 2000 times as much lift as a similar volume of H2 within Earth's gravity well, then you could put the flat-top on top and the hangers and much of the armament underneath to provide the needed balance to ensure it didn't go belly up.
In ship design terms, this interaction between top weight and buoyancy is called the metacentric height. If it is positive (i.e the CG is below the Centre of Buoyancy[CB]) then the ship stays upright. When the CG gets above the CB, the ship turns turtle. Ships in the North Atlantic run the risk in winter of putting on so much weight in ice on the superstructure that they _do_ turn turtle. It has and continues to happen.
The further the CG is below the CB,the more stable the ship is, but the deeper it sits in the water and the more energy it takes to move it. Warships tend to run with a very narrow margin between the CG and the CB to minimise drag and increase efficiency and so have to continuously watch for things like winter ice or too much mass above the waterline.
And I'm sure that is waaaaay more about this nonsense than you wanted to know. :)
Ship Design 101 is now over, class dismissed.
Paul