We could always argue that the ability to raise the wings is crucial for giving the ship the ability to land - and the very reason this ship exists in the first place is that it is a landing-capable addition to the Klingon fighting arsenal. Up is necessary for landing; let's assume down (rather than horizontal) is necessary for flying in an atmosphere (because a bit of anhedral in the wings is a valid aerodynamics trick for creating stability in certain cases). The skippers can then choose whatever position they wish for spaceflight, where all positions are equal - and some prefer horizontal while others like down, perhaps because they have different ideas about whether to take the fight down to an atmosphere if one happens to present itself during the fight.
It would also make sense for the Klingons to have at least two sizes of ships that can operate in an atmosphere and land and take off. Perhaps it is
a good idea to build both designs to the exact same shape? That is, in space, shape is irrelevant - but in atmospheric flight, the engineers would have to do new calculations for a new shape, and they decide not to.