Horizontal and vertical are irrelevant without a horizon as a frame of reference. The only two clearly defined axis are thrust and normal. Either the ship is long and narrow along its vector of thrust, or it is broad and short in its vector of thrust. If you rotate a "vertical" ship 90* along normal, it would look as a "horizontal" ship but behave identical. The only consistent frame of reference is the vector of thrust.
The main arguments for coaxial ships are that you expose as little front towards the enemy as possible and that you have the greatest possible length of weaponry such as mass drivers.
The main argument for conormal ships is that you have the maximum surface towards the enemy for mounting equipment, and a larger surface for mounting engines.
Conormal ships are more common in softer science fiction, as they in most depicted space battles are inferior to coaxial. But there are techs and tactics that could use conormal ships to great effect. They turn faster, and several smaller guns might be more useful than a few bigger. Depending on what phelbotinum you are using for shields it also reasons that conormal can have more shields, offsetting the increased chance to be hit.
Perfectly round ships expose the minimal surface/size if the enemy is equally likely to engage from any direction, but we can assume you can orient your front quickly as well as choose engagements where it already is oriented towards the enemy, and thus spherical ships expose more surface/size than coaxial on the whole.
So you can either have shape of ships be fully aesthetic or you can have it as an option for chassis, with accompanying bonuses and penalties.
I personally think that coaxial ships are the way to go and they got it correct in the anime show 'Legend of Galactic Heroes.' (Heh, no bias here given my avatar.)
All weapons are mounted at the bow, and the rest of the ship 'hides' behind them. This way, the cross-sectional area avaialble for enemy long-range bombardment to score a hit is minimized, and the deflector shield power can be concentrated in a small area.
Downside is that if the enemy succeeds in maneuvering to your broadside or forces you to fight with your broadside exposed towards them, your cross-section grows enormously, and your fleet suffers a disproportionate casuality rate. In fact, outcome of many battles in the show is determined by successful fleet maneuvers to land bombardment on enemy's broadsides.
This being the reality, conormal ships (horizontal and vertical) would not do well in combat.
(There are things that this show gets completely wrong too - melee combat, lack of mobile communication.)
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