According to a science page at
http://www.freemars.org/jeff/planets/Luna/Luna.htm , Earth's moon is about 3,476 km in diameter, or 3,476,000 meters across (notice the "k" which stands for "kilo" or a thousand in "km"). A spacecraft even a thousand meters across would have a shadow 1/3476th of the diameter of the moon, or, in other words, so tiny that looking at the entire moon it would be so relatively small it would not be seen.
If you still don't believe me, try rendering the whole thing in the software with the moon larger to approach the proper scale of the ship relative to the moon (Don't go exactly to scale, I'm guessing the computer wouldn't handle it, I'd suggest even just twice as large) and you will see that the shadows from the ships will shrink more and more as you approach the "real" proportions of a ship several hundred meters across to a moon several million meters across.
This assumes that the moon in the render is the size of Earth's moon, but even a smaller moon would be so large that the shadows would be relatively so tiny they wouldn't be seen.
According to what I've studied in Astronomy class at college, tiny moons (where a shadow from such a spacecraft might be visible) would be more like asteroids and would be irregular in shape, not spherical, because of a lack of enough gravity to compress into a sphere.
Actually, our moon is a little egg-shaped, not a perfect sphere.
The situation is different because Earth has an atmosphere which refracts light (think of the way light behaves in a fog). The moon doesn't have an atmosphere at all, so sunlight doesn't get refracted and the lighting as a whole is much more direct.
Actually, if you really wanted to be accurate (or downright picky), our moon does have an atmosphere, it's just extremely thin because of the much lower gravity (Another thing I learned in the same class at college). Even space between solar systems isn't completely empty, there are occasional particles of various junk that are microscopic.