This trope is probably going to be Truth in Television for military spacecraft in the near-future (with the earliest favoring the tinkertoy/habitrail/industrial plumbing aesthetic of the International Space Station), just because of the limits of our launching methods — cylindrical rocket sections bolted together in space. Eventually, though, it may become a relic of the near-present as space-based construction becomes easier. In space, there is no gravity or air resistance to design around, and due to the distances involved and other factors visual camouflage probably won't be much use either. The habitable sections of these spacecraft are not likely to be "boxy," due to sharp corners being weak points when there are high differences in pressure between the interior and exterior (the same reason why airplane windows are rounded and not square). Historically, armies put quite a bit of thought into looking good and only stopped when it became necessary to do so (the British Army switching to khaki uniforms after the Boer Wars, for example); given the chance, it's likely that looking grand will be back on the agenda. The engineers will probably hate it, but then again, they probably won't be controlling things. On the other hand, in this modern, cost-conscious world, the accountants might have a thing or two to say about wasting money on decor...to say nothing of what happens when news gets back to the Federation Parliament...will the voters ever have a fit when they hear about the gobs of cash being spent to paint their ships in gold for no reason other than "it looks pretty."note
Existing spacecraft have so far had a mixed record: modern rockets and atmospheric landers tend to be white and aerodynamic, but blockier than sci-fi space fighters and only sometimes winged. Craft designed solely for vacuum are totally unaerodynamic, but extremely spidery and jumbled, covered in reflective foil (for heat management) and held together by networks of pipes and struts, looking much less solid than sci-fi capships.
On the other hand, the products of the emerging private spaceflight industry often feature curvilinear quasi-retro stylings which bear a close resemblance to early sci-fi rockets of the zeerust school. Contrast the lines of the Scaled Composites SpaceShip series with those of the Soyuz capsules, or even with the Space Shuttle. (Mind you, the SpaceShip series are just pop-up suborbitals, and reentry from Mach 3 (SpaceShipOne) or 4 (SpaceShipTwo) is between 40 and 70 times less energetic (and thus easier) than reentry from orbital velocity. SpaceX's Dragon is orbital, and quite chunky-looking. On the other hand, an SSTO usually has enough empty space inside to greatly ease the pain of reentry, and while you can still get fairly blunt designs, you can also get this...)
Also, some of these designs actually make some sense. For example, after the first two missions NASA decided to leave the external tank of the Space Shuttle un-painted because of the extra weight that pretty white veneer added (to give you an idea, the paint on a 747 jetliner weighs hundreds of pounds), not to mention the fact that it all burned up when it fell into the atmosphere anyway. For deep probes our designs are pretty non-blocky only because they are not meant for any kind of combat. Wings may be used on craft intended to work in atmosphere as well (like BSGs Vipers), even though it wouldn't probably be very practical to make a dual-purpose craft like that given the hugely different conditions, especially when considering the different atmospheres and gravities of alien worlds. Unpainted metal or reflective exteriors may also be justified if the ship is intended to fly near stars: this would reflect the light assist the ship in staying cool, similar to the way that skyscrapers in the southern USA and other hot places tend to be designed with reflective glass exteriors.