MA.le:
You've asked about one of my favorite topics. Wish I had the full answers!
I am not sure if I understand exactly what you are asking in regard to the "structure" of Sanke sumi vs Showa sumi. I do believe there is a difference, at least so long as not looking at those Showa whose genetics have become more Sanke than Showa. But, I think the main difference is in the molecular structure and placement of the pigment within the cells of the skin layers, but there may just be a difference in the pigment itself. It is a question of the density of the pigment. Over 20 years ago, Japanese researchers described the melanophores of carp as being like a woven basket. They leak melanin (black pigment), like water placed in a basket. If the genetics result in melanophores with a very tight weave, the skin darkens. If the melanophores are close together and "tightly woven", you will see a black spot on the skin. For the genetics to give you the visible spot of black, the proper raw materials must be present. One is silicon. Hard water is typically high in silicon. So, you will be told that hard water is good for sumi development.
Cell structure is just part of the equation. Another part is the skin structure. In young fry there is often a camouflage of black pigment which fades away after several months. Such "baby sumi" is in the uppermost layer of the skin. There are at least two theories about why the sumi fades. One is that as the young fish grows, the melanophore wall stretches, allowing the melanin to diffuse. Closely related is the idea that the melanophores in such fish simply dissolve. Another theory is that the fish is genetically programmed to produce less melanin. All of these notions may be correct in one specific instance or another... or maybe all are wrong.
We often talk about sumi rising, as if the sumi is in a lowermost level of the skin and is coming up to the outermost layer. This is not a physically accurate idea, although it is very poetic in describing what we see. (JR has commented a number of times that what is occurring is consolidation of black pigment, not movement of the pigment through the skin layers, but I like the visual impression of the phrase "rising sumi".) What occurs is the thickening of the black pigment in the skin... melanophores "filled" with melanin and in close promity... a profusion of melanophores. And, this pigment need not be limited to a single layer of the skin. Think of there being melanophores in just the top layer in one fish and in three layers in another and in only a middle layer in a third fish. The sumi will be blackest where it is both concentrated in a layer of skin and thick in the sense of several overlying layers of such black skin. Query: Where the sumi is relatively concentrated in just a middle layer, is the visual effect what we call "kage sumi"?
Now, think of structure in another way. If you look at the typical Sanke, you will see that the sumi appears in a series of tightly concentrated specks which give a mottled effect that gradually becomes a nice solid spot. I call it "confetti"... as if overlapping pieces of black confetti finally become so numerous that the mottled effect gives way to solid lacquer black. Shiro Bekko show what I mean very well. In these fish, the melanophores align with each other in a particular way. In comparison, Showa have what I call "watercolor sumi". The melanophores are more loosely aligned. There have to be at least 5 different sumi concentrating behaviors in Showa. (See the "Rainbow of Showa" thread where I've been tracking some Showa.) Going back in time, the tendency was for Showa sumi to concentrate slowly in the thin outer layer of each scale with the deepening pigment being greater at the edge of each scale, giving the impression of watercolor pooling at the edge of each scale. This would be occurring either before, after or at the same time as the sumi concentrated in the skin around the scales... giving many different impressions to the human eye.
As Dick pointed out, good Sanke sumi has a blue-black cast to it. In early Showa, the sumi was more brown-black. The "confetti" structure of melanophoes in the skin seems to be linked to the blue-black pigment. The "watercolor" structure of melanophores seems to be linked to the brown-black pigment. Today, Showa have been so cross-bred with Sanke/Bekko/Kohaku that these generalities are less true than in the past, and perhaps best seen in the least desirable examples of the variety.
Well, I'm running long to the point of drivel. But, one more thought: Asagi. The blue scales often take on their color in a "watercolor" sort of fashion, while the unsightly black specks that can mar an Asagi appear more "confetti" like. Asagi are at the root of everything when it comes to koi.