Thank you for explaining just why you think it's so stupid. I assume that it's because it would be better to treat the neck of the ship like an axle rather than a fork for a spindle. I'd say a reasonable argument for orienting the disk like it is that it decreases the frontal area of the ship, meaning that the ship is less likely to run into debris at speed, and one could say that by being able to place the nacelles closer together would allow for less energy usage in the spacewarp process.
Plus it looks prettier than either a sphere or a front-facing disk/wheel. At least I think so.