The most common X-ray diffractometer uses a flat stationary sample holder, which is referred to as Bragg-Brentano geometry.

For such a stationary diffractometer, the intensity of a Bragg reflection is proportional to the relative number of crystallites in the sample that happen to be in an orientation with the hkl plane parallel to the sample surface. In this geometry, only those crystals will diffract the incoming xrays that happen to be oriented with the respective (hkl) plane parallel to the surface.

If all crystals are randomly oriented, this probability is independent of the indices hkl. If on the other hand more you have preferred orientation, a group of lattice planes will be more likely to be parallel to the surface compare to other reflections. The relative intensity of Bragg reflections of this group of lattice planes will be increased compared to that of other hkl groups.

In your case, if the diffraction pattern shows only 200, 400, 600 that means that the direct space direction [100] is very much preferentially normal to the sample surface. Other directions like [111], which is normal to the hhh lattice planes are much less likely to occur normal to the flat sample surface. Accordingly their intensity is diminished. As you state that you observe h00 reflections only, your sample has a very extreme preferred orientation.

It does not tell you anything about stacking of a 2D material. The preferred orientation tells you something about the orientation distribution of the crystallites, not their internal structure. If your 2D- material consists of layers which are parallel to the h00 planes of the bulk material, the material is most likely stacked with such layers parallel to each other.