Most of the headstones in the WWI cemeteries have crosses on them. The Americans, French and Germans actually use a cross-shaped stone as the marker.
Every so often in the American and German cemeteries I was in (back in '07) I came across a grave with a Star of David headstone. And, in the French cemeteries I saw some for their Muslim dead. But, how did they mark atheists' graves? I never came across anything that might have answered that question.
The British used a rectangular-shaped stone with a rounded-off top rather than the cross-shaped stone. The British headstones have a cross (or Star of David) etched into the stone. However, it was only in the British cemeteries that I came across stones marking what might have been atheists' graves.
Obviously, I have no way of finding out for sure, but this grave of a soldier from the Royal Irish Fusiliers looks so bare that I just assumed he had made it known that he wanted no cross or any religious marker on his grave. And they say there are no atheists in foxholes.