They exist because, like Minecraft, this game is a SANDBOX, and not an MMO, which is a detail you seem to be forgetting. If Starmade were going to go down an MMO-like path, then this idea would have some merit, but it doesn't.
Some people don't have problems with these things or enjoy throwing together something easy so they can do other things that they enjoy better. I know I'd rather be out mining than working on an extravagant house (In Minecraft), The same thing applies to starmade, where some people would rather be able to throw something together so that they can kill pirates or defend them selves from players with titans that threaten their home without spending days working on it just to see it get blown up.
I partially agree that having the ability of quicly and with little effort put together a functional ship is a good thing, though it doesn't necessarily become significantly harder with reasonable system shape restrictions (or should we say enhancements if a certain shape improves efficiency?). However, the real reason for doomcubes is EFFICIENCY. It's the most efficient way of making ships and on top of it, it's fast and easy. There's no need or incentive to build different unless you want to make something just because, and if you do, you are penalised because the shape is not optimal.
Restrictions in a sandbox game will lead to a loss in beauty and creativity, not a gain in it, because it will harm the people who like to get creative with their stuff, and only push more people away from the game who can't build to a good standard. I like having the creative freedom to say "Hm, I think I should put most of my weapon in the back of the ship, and have a part that leads to a frontal output through my shielding system" and not get penalized for it.
and fairness, hah, a game where everyone is equal is boring. then it all comes down to just how good you are at the game, which alienates newer players, for instance, let's take an example. Most Minecraft PVP games have you in a preset class with the same armor and weapons as anyone else. the people with the most PVP experience will pretty much always win, with new players not able to keep up. I don't think anyone would want this for a game that hasn't even left alpha yet. You'll push new players away.
First: how is it ok for anyone thinking, "hmm, I think I should build a ship that's not a cube" to be penalised if your example of having most of weapon module blocks at the back is not? Putting the weapon blocks mostly in the rear probably wouldn't even be impossible, it might not get full benefit from the leading "barrel" blocks but otherwise it could be just fine, maybe 5-10% drop in efficiency for cool factor for the gun only. I don't think that's nearly as bad as the penalties for suboptimal shape atm. It doesn't matter what the ship building restrictions are (and there are some, even now even if you refuse to see them), someone is always getting penalised for not adhering to them.
Nobody is going to force you to certain ship or shape, not in vanilla game anyway... so comparisons to forced gear minecraft pvp is kinda off. This is already a skill based game where you quickly learn that cube is the best shape and looks don't help you in combat.
on top of all this, read how the game is advertised on steam: "StarMade is a voxel-based 3D sandbox space shooter. Play in your own universe or on a multiplayer server. Participate in epic fleet battles, strive to dominate entire galaxies and harness the universe’s resources for your industrious empire or the destruction of others. The universe is yours!"
Not anywhere does it say ships are/should restricted. In fact, it pretty much implies you can do as you wish. This includes building a doom cube.
I think that goes with the description of a game in general. All games have rules and framework in which they work. This one isn't without rules, they just happen to be geared towards minimal ship design right now.
Let's be clear though: You can't force creativity or prettyness upon people, it just won't work. Whatever shape restrictions may in future apply for systems, or some other features of building that encourage building in different styles, there will always be cubeblobs of modules because they are fast and easy to build and probably never going to be so suboptimal it's not worth it in a pinch, and probably some won't bother to build better because they don't want and ultimately need to. However, reasonable requirements for block placement can lead to ships having some sort of shape and encouraging some aesthetics without penalising them as much as it is now.
If a smartly built ship can go toe to toe with a reasonably designed, slap stuff together doomcube 10% bigger and both trounce a badly designed ships, then I'd consider it a pretty damn well designed build system. Smart ship design is probably never going to be very special or frilly, but that's just life. Pretty isn't efficient anywhere most of the time, although functionality can be good looking like the prettified cubes linked above
still, those would be better without the flashy stuff...