...in SE you can do research to improve the capacity of your hulls, thus allowing you to stick more components into the hull instead of having to use better components.
This is poorly defined, but if you mean that improving hull capacity should be a many-stage, ongoing incremental process, this is not a good idea. Suppose each time you researched an improved hull capacity, you got something like 10% more space on that hull type. This would have many of the same problems as miniaturization as a refinement for ship parts: in particular, it would mean that every time you refine a hull type, you would have to redesign all your ships to make use of it. This would not be not a good system, as it would require lots of busy work redesignings, produce lots of similar but slightly different ship designs to keep track of, and make it more difficult to define equilvalence for ship upgrade purposes
It's unlikely that we'll have a great variety of hull sizes, or a continuum of hull sizes. More likely, there will be a small number of discrete, fixed, fizes... perhaps 4 or 6, with names like Tiny, Small, Medium, Large, Huge, Colossal. This has the advantage of making the choice of size significant when designing a ship. It becomes necessary to pick between a small number of choices, each with well-defined and easy-to-understand properties, benefits and penalties. There is no way to incrementally enlarge hulls, so there's no need to change the layout of parts to do upgrades; instead, each part can be replaced with the newer version, when avaialble.
As to whether there are hull layouts separate (but within) the discrete sizes, which determine what type or layout of slots are avaiable, this is undertermined and up for debate. Having lots of hull layouts would likely mean having fewer sizes (likely just 4) to compensate. Each layout would be a distinct upgrade path for ship designs; you could upgrade the parts within a particular layout, but not change the layout of the hull. Each layout would have a set number of slots of particular types, with would never change for a particular layout.
Another issue is, assuming we base ship design around filling slots, where the slots have restrictions on the types of parts (engine, gun, armour) that can go in them, and or part size (small, medium, large), what's the rough number of slots in a design? There are two extremes:
1) SMAC-like designs with 1 weapon/functional, 1 defense, 1 engine, and 2 "special" slots. Each slot would have a size, and each part would have a size. The number of the chosen part on a ship would be qual to the size of the slot divided by the size of the part.
2) Effectively unrestricted, with (technically), limited slots, but in practice there are 30 or 50 slots on a ship, with these being all generic, with no per-slot restrictions. In this case, slots would essentially be stand-ins for mass or volume limits in the ship. Each part would require some number of slots to be added (ranging 1 to 5 to maybe 10 for really big parts). Ships would be required to have an engine, and perhaps one or two other "essential" parts, but there would be no restrictions other than this. It might not be necessary to even keep track of individual slots' contents in this case, with just a total number and number of occupied slots.
Somehting in between these extremes is also possible.
There could also be geometric restrictions, where each part consume some number of slots in some geometric configuration, with the available slots laid out in some hull-layout-specific pattern.
Also, note that as in the first post, long lists of how you'd like to put this or that type of turret on or descriptions of how turret size relates to chance to hit and ship size, etc. are not very useful. Please provide reasons for your proposed designs, or at least a few alternatives to consider.