Chickens will not really use a 'second story' unless it is totally different from the ground floor - as in the case of the previous poster's arrangement (and many tractors and small coops) where the house part is up on top of the run part.
If you put a second story *in a coop*, i.e. all indoors, they just will not use the upstairs very much. A little, but not much. I would not suggest counting it towards real-world square-feet-available-per-chciken.
(I am not sure what you mean by 'hammock' but chickens do not generally like walking on sway-ey uncertain surfaces, nor swinging perches either for that matter.)
So, I mean, by all means add vertical habitat complexity if you want, but I would strongly recommend making your chicken# decisions based on FLOOR space, i.e. the "real" floor only.
As far as headroom, I would not give chickens less than 24" and really you would want more than that for most chickens so that you can have a distinctly elevated roost. 3.5-4' is a good height for a reach-in coop, as it gives enough room to have chickens very easily walking underneath a roost and droppings board (if used, but I highly recommend it) and still have plenty of comfy headroom while on the roost.
Good luck, have fun,
Pat
