I was watching Star Trek, and I thought that the shape of the Enterprise is quite weird. So what do you think a big spaceship like the Enterprise would look like? We assume in this case that the problem with the gravity is somehow solved, so a tube shape is not necessary to leave the planet's gravity, as the ship will be built in space and will never enter the atmosphere. It has to accommodate about 1000 passengers.
Baring constraints imposed by the spaceship parts the shape would be either a sphere or irregular.
The sphere is optimal in the sense that it has the least surface area compared to volume. It also doesn't have any "corners" which is an advantage when it comes to maintaining a pressure difference. So a ship designed from scratch and built in space would probably be a sphere. This somewhat with limitations imposed by the spaceship components, for example if your engine is radiating strongly you want some distance between it and the rest of the ship - which can as an example lead to a ship that is basically two spheres with long struts between them.
If your spaceship is constructed in orbit it's also possible that it's essentially built by adding parts to it as and when those parts become available. In this case the spaceship would add parts at the points that is convenient at the time those parts where added - leading to a somewhat haphazard shape overall. For example the international space station. There is a problem with this approach in that your thrust has to be aligned with the center of gravity, which would be difficult. Essentially I do not expect anyone to suggest strapping engines to the ISS to create a spaceship, but it's not entirely implausible - especially if you have artificial gravity.
The shape of a vehicle depends on a couple of things, the size and shape of the powerplant/engine, the purpose of the vehicle and the aesthetic requirements/tastes of the customer/manufacturer.
The shape of the Enterprise is driven by the practical shapes of it's powerplant. The two engine nacelles are needed to gather enough interstellar hydrogen as fuel. Still in the Star Trek universe, the Klingons and the Romulans have different powerplants so their ship designs differ significantly from the Federation's. In every spaceship I can think of, the powerplant/propulsion system takes up a significant portion of the ship.
Purpose of Vehicle
A cargo ship will have a drastically different shape than a pleasure cruiser. A cargo ship wants to maximize internal volume for cargo. A small pleasure cruiser will care more about economy and speed. Look at the variety of shapes of cars/trucks on Earth's roads. They have radically different shapes depending on their needs.
The Romulans designed their ships around the shapes of birds. Maybe the customer really wants all chrome ships?
Necessity will shape space ships. We of course will start with big cylinders that rotate for gravity, I think that the center of the cans will be where the power-plant/propulsion system will be.
I think this might continue even if we figure out gravity fields to hold people to the deck. Partially out of inertia, we will have experience building ships that way and partly out a good design. the front of the ship can be designed to be a 'funnel' to help collect 'fuel' to feed into the engines, like a jet engine. This would have a two fold benefit. it would collect fuel and help protect the rest of the ship by 'guiding' harmful and dangerously fast matter away from the living quarters, forcefields would be used as the funnel.
If you mount the engines outside the body then you will have much smaller funnels guiding material and still need to protect the whole ship from collisions, maybe having to deflect the matter much farther to protect the whole ship.
As @BartekChom said you can have any shape. To elaborate, in space you can assume there's no friction so a cube would be as "aerodynamic" as a ship shaped like a rocket.
If your ship is a generation ship (will be travelling through space long enough that people will spend their entire lives on it) then you may want a ship which is a large sphere with different levels for the functions needed.
As well you need to consider how the ship will deal with threats, whether they be environmental or from other ships. Will it have a force field? Can the fields shape be manipulated?
The final consideration is fuel/propulsion. Does it use unobtanium to move, or will it need to collect the fuel as it goes. The engine is also important, does it require shielding, does it have a specific shape it needs like a solar sail?
Given your setup, most importantly the part about not entering an atmosphere at any time, and that it is built in space, i think a construction that looks like the ISS with the enterprises engine gondolas attached, is a very likely result.
The basic setup of the ISS, with everything built in (more or less independent) modules arranged around each other provides ease of build, since you can dock individual modules tio the cluster pretty much wherever it is convenient, and in case of a hull breach you only loose a single module (until it is repaired or replaced).
The enterprise-style engine gondolas seem likely to me because i assume that they might either be radioactive, or very hot, or have strong EM fields, and might have a risk of fires, explosions or similar, so that you might like the possibility of getting rid of them easily when necessary.
So, overall, you will get a fairly ugly cluster pushed by an arbitrary number of very, very large engines.