A spaceship which has to travel fast will find that space is not totally empty. It will run into space dust and space atoms, and loose space electrons and protons and it will run into photons of light which will be blue shifted to higher and more dangerous frequencies by the doppler effect.
So the faster a space ship has to travel, the more it should be a narrow cylinder to minimize the front surface that impacts particles and photons.
And the internal layout of the decks should be more like a skyscraper than like a ship at sea. The decks should be circular, and perpendicular to the direction of travel. So if the ship has artificial gravity generators the direction of up and down will be parallel to the direction the ship travels. If the ship accelerates or decelerates, the artificial gravity generators will increase or decrease their output to keep the gravity felt by the crew steady. If the decks were laid out like on a ship, the artificial gravity generators would have to adjust their angle by 90 degrees as well as changing their amount of force. That would be much more complex.
And if there are no artificial gravity generators, a layout of circular decks at right angles to the direction of travel instead of long decks in the direction of travel would be even more necessary. If a space ship had long decks in the direction of travel, and someone was walking in a large fore and aft corridor when suddenly the engines started firing and making acceleration, they would find themselves falling down a large shaft to their death.
Anyone who has ever seen The Black Hole (1979) should realize how silly it is for the Cygnus to have the layout of a ocean ship with decks parallel to the direction of travel and rocket engines at the back. There is a corridor that looks thousands of feet long on the Cygnus. If someone is in the corridor when the rockets fire hard they will fall to their death at the back of the corridor, possibly breaking through the rear wall and damaging the engines.
I remember an A. E. van Vogt story from the 1960s, where the protagonist suddenly turned on the rocket engines, turning the rear bulkhead into the floor, which the antagonist slammed into.
It is quite possible that a spaceship would be a tall, narrow cylindrical framework of struts, with engines, fuel tanks, machinery spaces, crew quarters, etc. in various spherical, cylindrical, conical, etc. structures within the framework.
And in most cases there might not be any strong reason, except aesthetics, to put hull plating allover the main cylindrical framework, as Michael said in his answer.
Even in a space war, if two Earth colony planets with the same technology and with spies go to war, there may not be any reason to hide the various sections of a warship with opaque hull plating. The enemy may know from spies exactly how far along the hull of a warship the most vital areas are.
But in a space opera with many unknown and possibly hostile civilizations in the galaxy, there would be a possibility of of having to fight a civilization which has no prior information about the layout of your space battleships. Thus it would make sense to have opaque hull plating all over the framework of a space warship, so the enemy has no clue where the most vital parts of the ship are.
And if a spaceship normally lands and takes off planets which have atmospheres, it should have the entire cylinder covered with hull plating for streamlining.
I note that there is an floating platform, RP FLIP, which can mostly fill with water so most of of it sinks beneath the sea, and only one end sticks out of the water, for scientific research. And so the part of the ship which is inhabited has to have chambers designed so that two different sides can be the floor, depending on the position of the platform at the time.
And if the inhabited part of that ship were larger, it might make sense to put it on gimbals, so that the decks would always be horizontal whether the ship was vertical or horizontal or in between. Then researchers wouldn't have to adjust to the floor becoming a wall and a wall becoming the floor.
And possibly a large cylindrical spaceship might have the crew quarters and other parts sensitive to the direction of gravity, be spheres mounted on giant gimbals, within the hollow cylinder.
When the spaceship was travelling under power in space, or standing vertically on the surface of planet, the spherical sections would be in position with their decks at right angles to the direction of thrust or gravity, so that gravity or thrust would push down against the decks.
And when the spaceship was landed horizontally on the surface of a planet, the circular sections would be turned 90 degrees to have their decks parallel to the length of the ship and to the surface of the planet. Thus the force of gravity would push downward against the decks instead of sideways.
If a cylindrical spaceship has a height/length of many hundreds, or thousands, feet, it might be unstable in a vertical position on a planet, and so it might be considered better to land it in a horizontal position.
In A.E. van Vogt's Mission to the Stars the Earth space battleship star Cluster can break up into many smaller spaceship and then reassemble into one ship again.
I can imagine a spaceship made of tens, hundreds, or thousands of smaller sections or vessels, each with sufficient engines to maneuver a little. Each of the smaller vessels or sections might be square, hexagonal, or circular in cross section, and normally they would be clustered together in a configuration with a number of them side by side.
But when the spaceship made an interstellar voyage at high speeds, the sections would disassemble and then reassemble so that they were all end to end, forming a very long and narrow cylinder to minimize the cross section that would be hit by particles of matter and energetic photos at vast interstellar speeds.