I wonder if you've ever seen the Starfleet Museum
? It lists a whole range of pre-TOS ships which (in the early years) did indeed stack the decks in the way you describe. The first in line of these ships is the Bison
class, which I highly recommend reading.
As to fitting the decks into the Enterprise's secondary hull that way, the conical shape would tend to get in the way I think. As a result, the full radius of the circular corridor sections which could fit would be about the same size as Robert_Comsol
's ful circles on his Decks 12 & 13. This is quite a lot tighter than what appears onscreen.