I voted for long because I found the long ship look better and the stubby concept doesn't evoke much to me so far.
That said, the carrier needs to:
- have an easily recognisable shape, so a player can instantly identify it as a carrier (instead of a cruiser, destroyer or even corvette or station - distances may be hard to judge)
- look like something players can identify as "carrier", so it has to either respect SciFi conventions or have features that distinctively scream Carrier! at first glance
- look good
Traditionally, carriers are long and flat, probably due to resemblance of RL aircraft carriers, so people will recognise them as such. In addition, other capital ships are generally thicker and shorter to better show sturdiness and firepower, so the shapes are easy to identify. Inversely, long and thin instinctively shows that this ship isn't meant to take too much heavy fire, as a support vessel.
As such, long is the safe bet.
This doesn't prevent you for going stubby, but you may have to go further to make it distinctive and "carrier-looking". One solution would be to have big fat hangar bays bulging out of it, contrasting with the more regular "sturdy tombstone" shapes of the other capital ships.
As for what is more realistic, our ships already have magical god-knows-how-many-g inertia compensators, armour/shields and fuel-less drives, so I wouldn't pay too much attention to that for simply determining the shape itself. Having coherent justifications will be more important later, possibly once you work on the details of the models, but it can be made to fit the general shape.
Also, I guess it is too late for tower-shape capital ships? Now that the Expanse finally gave the general public an iconic image of vertical ships (as God and Heinlein intended), we can start using them in SF (while still having it stand out at the moment).
But I guess at this point of the design, it would require too much resources and time to backtrack on that decision.