Ah, here we are getting into histo-architectonics, the study of why one tissue is different from another, and so on.
For your reading interest, if you have not already read it, I would like to point you twoards Heido Braaks "Architectonics of the human Telencephalic Cortex". Sorry it is so dated, but Architectonic studies are all getting subsumed into the Brain Atlas projects, so many of the researchers in this area are not able to find the time to write a book on the new processes.
According to Architectonical theory, the laminar nature of the cortical tissues developed as an evolutionary effect, The first laminar elements were the hippocampus, which exhibits radial symmetry in its neurons, but has a unique seahorse like shape caused by penetration of a second type of processing system based on molecular neurons. Eventually this two layer structure was increased to three layers with the addition of a rich connection layer.
The three laminae structure then went on to populate allocortical issues. Or early cortex especially around the olfactory bulb. In the tissues that intervene between the hippocampus and modern isocortical tissues such as seen in the optic tectum, (that is part of the neocortex isn't it?) Braaks book has shown a distinct maturation from allocortical, to isocortical tissues during stages of growth of the cingulate cortex. Essentially soon after the hippocampus, a second cortical tissue gets overlaid over the first, and this results in first mapping between two systems of memory, and second, the integration of the two tissues into a single tissue thus making the isocortical tissue equivalent to a translator between two different types of memory. I call this the Dual Mode Cortex. And suggest that early allocortical tissues are implicit , and isocortical tissues allow explicit addressing of implicit memory.
Now on to the real question why is the hypothalamus not laiminated in the same way as the cortex?
Well evolutionarily speaking the Hypothalamus comes from a much earlier time, and therefore would tend to favor radial symmetry, and the Cortex Laminar symmetry. What I would expect to find in the Hypothalamus is a number of nuclei that each have a specific job. Any laminar effects would be like that of the Nucleus Accumbens that has an inner organ and an outer layer over it. Processing centers are likely to be ovoid, and so on. If you look closely the memory cells in these processing centers are likely to be the so called "Post-pyramidal" cells that look like disorganized, and spherically oriented pyramidal cells.