It's something that bothered me a bit about the resizing at first. But then I realised that the windows don't indicate decks at all.
Plus, it's really only noticeable in the dorsal and secondary hull, maybe all of those decks are two "primary hull" decks tall. The engineering spaces don't seem to have a traditional deck structure at all.
I'm cool with the 2x increase in the nuEnterprise's size, since they did the exact same thing with the original Jeffries ship.