Not nessecarily. Inertia is going to operate the same way on a ship wether its symmetrical or not, it just depends on wether the ship's structure is strong enough. Otherwise the ship would have to be perfectly radially symmetrical to avoid trouble. Look at the Colossus, for example. Its VERY assymetrical along the vertical axis, but can we realistically say that if we rotated it 90 degrees so that it was asymmetrical left to right instead of top to bottom that it would create more structural difficulty? Of course not.
The trick with an assymetrical ship is just to make sure that propulsive thrust is always aligned along the ships center of mass. Asymmetry creates problems when force is being applied to the structure off axis, because then it tends to apply rotational force instead of propulsion.
It is exactly right to say that we tend to find assymetrical objects less pleasing because we are symmetrical ourselves. However there isn't any structural reason why you can't make them that way, it just makes things a little more complicated.
