I'm not sure, but I think you're just seeing the bottoms of distant clouds. If you don't have something to cover the horizon, you'll see clouds extending far below the horizon because they curve downwards due to the curvature of the planet. If this is what's happening, then I don't think anything is wrong with it. The point where they stop is where the atmosphere's "floor" parameter blocks them with an opaque black sphere.
If your render is being cropped exactly at the horizon, then I think you're just seeing distant cloud curving down towards the horizon.
If you want them to fade into the distance like they would when an atmosphere is present, you can render with an atmosphere but use Render Elements to extract the cloud element (which will be darkened to black as it recedes into the atmosphere).