On the better carved beads in my necklace, the shallow holes relate to the tops and bottoms of leaf-like shapes. These holes are not very distinct (I missed them previously) and they give the carving greater depth (emphasis) surrounding the leaves. On the less well carved beads, triangles are substituted for leaves and the holes are totally random. These are the very distinct holes I saw earlier.
I'll take pictures to post tomorrow. Thanks all!