This is a bit of a frame-shift answer. I am answering as a space enthusiast, but also as a person at an aerospace company.
Let's not dismiss the simple shapes, such as cylinders, as hangovers from aerodynamics too quickly! There are some important considerations, even with plentiful material and practically no gravity, which may lead to simple shapes (cylinders, spheres, rectangular prisms) dominating spacecraft development.
Center Of Mass and Center Of Thrust
There are still virtues in aligning center-of-thrust and center-of-mass, like not spinning out of control! For those unfamiliar with these terms, the center of mass is the 'middle point' of all your mass, and center-of-thrust is where your 'push' from your engines points to. Not lining these up results in your spacecraft spinning, so something needs to be done to counteract this. A design which avoids spending more fuel to counter any moment/torque produced by oddly-placed engines on oddly-placed shapes will be preferred over others.
It turns out if you build a known shape, (such as a sphere, a cylinder, a brick) you have a decent idea of where the center of mass and center of thrust could be. This even accounts for odd loading! If you build an irregular shape, you need to do a lot more math to account for mass distribution and thrust. Depending on loading, even rockets with gimbals (ones whose nozzles can point) may not cut it on these eccentric shapes.
This issue gets compounded if the engines used cannot be throttled or more than one engine needs to fire for 'forward' motion. Odd shapes could easily rely on multiple engines for simple 'forward' motion to account for loading or structure. This introduces more failure points, which is a less robust design, which mean it will be less favored by practical design. Further, if the engines' output must always be full blast or nothing (no throttle), good luck getting 'backup' engines in the correct place. Simple shapes usually mean you need less engines for 'forward' motion and rely on modest gimbaling to account for a lost engine or irregular loading.
You Still Need to Build It
Hey, there may be a galaxies' worth of material out there, but you still need to put in the time and effort to build the ship. That still costs something; time, possibly money, and certainly resources.
It turns out simple shapes allow you to minimize the amount of material while still getting the volume you want. Okay, maybe ships will not always a brick or spheroid, but these shapes do have nice volume-to-surface area ratio compared to others!
Mechanical Stability Considerations
It is cool that your spaceship looks like an anemone, but it bends like one, too. That is not fun when your mess hall is on one tentacle, sleeping quarters on another, and your pilot is on another. Poor Bill had to wait until the acceleration maneuver was finished (which was a full year!) before the hall to his quarters bent back into shape. That is better than Steve- his tentacle just snapped off during the last emergency correction.
Maybe if the ship was a simple shape to bear the loads of thrusting and maneuvering, issues like this would never happen. Something like a spheroid or rectangular prism... These shapes are capable of supporting themselves with less material and clear load paths when compared to something more spindly.
A more robust shape may allow for more aggressive maneuvers for less material (or 'primary structure'). Less primary structure means more room for payload or yet higher acceleration maneuvers. Overall, these things are desirable for most spacecraft.
You need to be careful about your thermal control surfaces. If a radiator (to get rid of excess heat, one of the only ways in space to do so) is next to your thermal camera, all you will see is your radiator. How do you avoid this?
You choose a shape which have surfaces pointing away from each other. Spheroids, cylinders, and cubes do not have this issue. The other solution is to have 'cleverly placed' sensors, which does open up some possibilities for odd shapes. (See ISS- not all of those panels are solar panels!)