The neutron scattering on a two-dimensional ordered nanostructure with the third nonperiodic dimension can go beyond the Born approximation. In our model supported by the exact theoretical solution a well-correlated hexagonal porous structure of anodic aluminum oxide films acts as a peculiar two-dimensional grating for the coherent neutron wave. The thickness of the film L (length of pores) plays important role in the transition from the weak to the strong scattering regimes. It is shown that the coherency of the standard small-angle neutron scattering setups suits to the geometry of the studied objects and often affects the intensity of scattering. The proposed theoretical solution can be applied in the small-angle neutron diffraction experiments with flux lines in superconductors, periodic arrays of magnetic or superconducting nanowires, as well as in small-angle diffraction experiments on synchrotron radiation.