Every ship design should be dependent upon the function, so I don't think there will be a single efficient design that suppresses creativity. In 3D space, everything is relative to the expected situation. Generally your goal is to not get hit, and if you do, you protect where you think you will get hit from. A cube is an all-around generalist design that will basically be good at getting hit all over, but that means less armor in any one spot. A ship design that can always keep it's front pointed towards a target would do better to have extra armor in the front - however, a flanking ship would be able to target any weak points.
If you are a merchant ship, keeping cargo and armor to the back of your ship protects your cargo and if you lose the cargo to a pursuing attacker, you gain speed and can get away. However, if caught out from the front, you're weaker and more prone to taking critical damage. A clamshell style ship can maintain heavy armor on two sides, fitting guns and less armor in the middle, meaning they would be a smaller frontal target, balancing their weakness to head-on fights where an enemy could target the middle of the clamshell; the strength of the design being able to deal with flanking damage with ease.
A sphere fighter would be able to conceal some of its movement properties and present a more static profile, but one which you're not able to easily anticipate movement from. It would be like shooting a wobbly ball. This suffers somewhat like the cube ship, in that you're fairly protected from all angles but not the best at any angle. In addition, the poor use of space in a sphere ship would be hard to fit everything you might want into it, increasing the overall size due to inefficient space utilization.
If you have a large fleet, lots of hammerhead style ships with front armor, acting like a shield protecting rail-gun ships in the back of the fleet, means those mass-heavy ships have a purpose, and will be good for that purpose, but again if a squad gets behind you, those ships become a slightly softer target.
It boils down to some interesting balance, because if you think you will be hit at from any angle at any time, a sphere or cube shape ship is very generalized and should perform well - in doing so you are less-fast than one specialized ship, and can't take as much damage as another specialized ship. However, if you learn to control one facet of the fight, such as being able to keep a target to your front at all times, you can build to maximize your potential knowing those conditions.
There is no one best ship, though out of convenience, cost and other factors, we might see fairly generalized 'good enough' ships. The key will be to balance cost to produce with effectiveness and so on. If you're throwing endless cheap ships at a target, then a lot of 'guns with engines' becomes more viable than worrying about protecting anything or how it looks. So the economy will play a big part in making sure people design for what is worth it. A high cost of production will mean bigger, more armored and slower ships, while a balanced cost would see every variation.
Last I'll point out something we'll all probably enjoy a little - mining. Is it better to use a very fast, lightweight ship that can get to the asteroid fast, and get back to station fast, or a large ship that can scoop up multiple asteroids at once but is slow? If you think about it - if both of these methods produce the same amount of resources returned to a station over the same amount of time - there's no "best" ship for this. The fast small ship might be able to sell their haul at a higher profit each time, because they can deliver lots of small packets of resources to the station, not affecting the price of any one material too much, and capitalizing on their valuable mined materials more because they get to sell their product first. The larger ship however can haul back lots of material, necessarily dropping the price heavily when they sell in bulk, but having a much higher bulk payoff per trip. The smaller ship would spend a lot of fuel, going back and forth, countering his higher profit, where the larger ship would spend less fuel, countering his lower payoff (and maybe do less overall manual work). The faster ship might be able to deliver highly sought after materials quicker, while the slower ship might be able to deliver bulk materials to someone who needs a lot of stuff all at once. So it's fairly balanced if the game systems can achieve that balance, and each method for doing this will be different based on who designs the ships and so on.
It comes down to preference. You might like a ship that flies "down" or "horizontal" while you're sitting in the cockpit, where your perspective is facing "up". This would allow you lots of vision for mining, or aiming weapons and so on. That preference will be viable for the style of flying you do and the kinds of things you do. If your ship easily moves "up" and "down" relative to your view, you can pop out from behind asteroids or other ships to take shots, and then quickly move to cover as needed. This means your style of play and your creativity will give you an edge depending on the situation.
In the end, most people will not be inspired to create their own ship, so the diversity will only come if we have enough people making their own ships, in their own factions, and if production cost is high enough where you can't just buy one of each car on the car lot. Most people will just want whatever works (or whatever they can afford), and this will help the economy and allow ship builders to make and sell their ships. So even if it looks a little bland at some point, as lots of people really like one style of ship, keep in mind that it's just a fad; that the moment some conflict arises, or the moment someone realizes something new about the game, the designs could shift dramatically. If for example, someone spots a mega-asteroid far in the distance, the focus of ships will turn to fuel storage and distance and so on, to go check out what that thing out there is. Luckily, as shown in the Boltcracker video about sabotage, we can just slap some fuel containers on our ships and begin our journey... only to be taken out completely by some guy in his default Kingdom fighter...
Edit: I forgot one thing: one way to make sure ships are NOT unique is by implementing sci-fi 'shields' that protect ships. Then the look and shape and purpose of the ship goes out the window at that point. Further, if the devs ever add planets with atmosphere into the game later on, this would dynamically change the meta ship for those areas - maybe specialized ships which operate in-and-out of atmosphere with ease would perform better around those planets, but less effective in open space. Anything that changes the environment would shift ship design, so gravity wells would make certain ships better in those environments, nebulas would see different ships and so on. I think a key thing to keep an eye for is you don't want one ship completely invalidated by an environmental factor - just have it more efficient if you chose something purpose built for that environment.
