Ok, not holding my breath on thicker atmospheres as that would be new DLC huge.
Not necessarily, if we leave Earth-likes out from the equation. All that would be needed for barren thick-atmosphered planets or gas-giant skimming would be clouds, precipitation, wind (things MS flight sim has done for decades so not exactly ground-breaking) and tweaking of ship flight models so they would handle differently in thick atmospheres.
That said Gutamaya, Saud Kruger and Zorgon Peterson look atmosphere capable.
Saud Kruger—not terrible, but those wings are way too small to generate any appreciable lift. And the, ahem, cigar-shaped hulls are no good for lift, either. At least the hull shape is reasonably low drag (some greebles though) and the center of pressure is behind the center of gravity. In short, they only need to fight gravity, not drag or instabilities.
Gutamaya—they look sleek, but they're bricks. The many greebles and weird shapes would generate a lot of drag and it looks like the center of gravity is way back.
Zorgon-Peterson—as I said, Adder and FDL are fine. Hauler is a brick. Mamba has low drag, high lift body but these two flat prongs in front of it would move the center of pressure way forward causing severe pitch instability.
Lakon—Asps would be guite good, the body would generate decent lift. The rest are bricks.
Core Dynamics—all bricks, but not the worst bricks. Corvette hull would have pretty good lift hampered by high drag of all the greebles. FAS/Dropship/Gunship would need to fight the gravity and drag, but the wings would provide decent maneuverability.
DeLacy—Anaconda and to a lesser extent Python are bricks, the rest are pretty good lifting bodies, especially Sidey, Cobra and the Kraits.
The Eagles—somewhere between bricks and lawn darts.