It's complicated. There's no real reason you couldn't, with proper technology, make a very large spaceship. A larger ship could be much more efficient then several smaller ships owing to economies of scale. (Cargo ships are much larger then trucks because they can be made so practically, with the limitation being the amount of cargo that realistically needs to move from one point to another and the water they travel in. In space, the only real limitation would be the amount of cargo that needed to be moved.)
But..
40k ships are stupid as shit. They must rely on humans to perform many task, including those better handed by electric motors, and so should be limited to very, very small sizes. If you can't build a 50 horsepower motor you can't build a spaceship, full stop. It's a retarded setting if taken literally, and instead should be looked at as a parody or fantasy.