KH - Why Perpendicular Deck Configuration?

I always recognized, and most of the time used, the original KH concept of starship decks being perpendicular to the ships axis but never gave it a lot of serious thought. From an earlier discussion in another topic's explanation about ADF using hard science examples, this placement of decks makes a lot of sense. However, I would like to try and reconcile this if possible with the common sci-fi media concept which often uses a horizontal to axis deck arrangement much like that of modern millitary naval craft. I hope the community can help me out with some thought provoking discussion here. Can horizontal deck placement be used? If so what hard science would be needed or support this (conventional or speculative)? How are atmo capable vessels with perpendicular deck placement effected by flying horizontally when operating in atmo?, and finally thoughts on why most artistic depictions seem to be of horizontal deck placement and how to reconcile to keep with the continuity and spirit of the game's vision. Thanks meet me at the new topic to discuss.