I have completed all the research regarding funnels, control station while playing as Germany. Yet some parts do not show up in the ship constructor when choosing to design a Superbattleship II (yet they do in the main menu ship designer).
For example, In the main menu ship designer I have options ranging from Uber funnel V-VIII and secondary tower options ranging from modern sec tower IV to Advanced tower with funnel mount IV on a ship with 1945 tech (see screenshot).
However, in game even though I have "very advanced" tech levels and have completed all research (boiler upgrades, control towers etc.) I have much more limited options. Here is what I get when I open the "New design" window via the ship desing tab.
Only funnel options V-VI and the advanced tower with the funnel option is missing.
I suspect they are not coded into the campaign files or there is some bug that prevents them from showing up.