Artstyle guide:Overview Guide
Retro thrusters, retro thrusters, retro thrusters, retro thrusters! (to the tune of "Developers, developers, developers!")
If your craft is: A) not Rlaan manufactured and B) more than 5 meters long it probably needs retro thrusters.
Now, the retro thrusters and maneuvering thrusters don't need to be necessarily as pronounced as the rear engines (giving you some artistic license in defining a visual front/back) but they NEED TO HAVE VISUAL INDICATORS OF THEIR EXISTENCE. For some ships this is mainly a texturing question. For larger vessels, this will necessarily influence your model design.
One of the biggest problems in space is heat dissipation. VS spacecraft have a lot of heat to get rid of, so they're going to need radiators. While, as with retro and maneuvering engines, artistic license is granted in how much of the ship's surface area is going to be radiator dominated, the same need for visual indicators of radiators exists. If you have fins, you should probably put a radiator texture on them, because they're almost certainly not for aerodynamic flight.
VS ships aren't, in general, intended to be very dense. This is more true for larger craft than strike craft. In general, the idea for VS ships is that the surface-area to internals ratio should be pretty high. The bigger ships in VS can be seen as big shells of armor and radiators around many, smaller, internal components. Moreover, a lot of the internal components would actually be plumbing, of the coolant (I always had a soft spot for gallium alloys, but no decisions are finalized on what exactly the coolant is) circulating variety, running between the reactors/engines (the engines being fusion reactors themselves) and other heat-generating components (e.g. weapons). The rest of the space being taken up by insulation (vacuum is pretty good) and physical shielding to keep the crewed and other sensitive parts of vessel safe from the engines/reactors, and other hazardous portions of the ship.
Most spaceships in the VS universe, even if capable of accelerating to escape velocity, are not designed for atmospheric flight. Some are. If its role description mentions "Aerospace" or "lander", "puddle jumper", "dropship", "ground support", or "orbital" then it's a good bet it has an atmosphere-friendly design. If not - build a spaceship, not an airplane.
That said, some smaller craft that are not atmosphere-friendly will still be atmosphere capable. The more developed the infrastructure of the group using/designing the ship, the more likely they don't intend for it to ever see atmospheric use on an inhabited planet - this is what docking stations, space-elevators, orbital shuttles, and other infrastructure exists for. In fact, (once we get planetary structures squared away a bit better), the really industrialized planets will probably start firing on you if you attempt to land in anything larger than a pinnace/dispatch craft, and even then only with appropriate permission. On the flip side, if it's a Forsaken ship, or a Luddite craft, then it probably spends a lot more time visiting places without well-developed orbital infrastructure and may need to land on occasion. Also take into account the age of the design you're considering. Much of the VS universe as of 3276 is post-frontier, but a lot of places don't have to think back too far to remember when they weren't. Use your better judgment.
If the ship is very large, even if it is atmosphere-capable, it is almost certainly _not_ atmosphere friendly, unless perhaps it's something very esoteric (atmosphere skimmer for terraforming project or some such). In general, if the ship is very large, it's best to assume it's not even atmosphere capable unless there's a very good reason for it. Large vessels will make use of shuttles and dispatch craft to take care of business on the ground.