You said: >>The hull needs to be strong where the centerboard well is located
I'd have to agree... except that the hull is already strong where the well is already placed in the aft position on most cats and since the forward position would be close to the main beam, I would guess its already pretty strong there as well so although it might need some reinforcing it shouldn't be a major obstacle...
You also said: >>Two centerboard wells on each hull means more weight
I'd have to agree... except on long legs of a course or cruise the relatively small amount of additional weight that would be introduced might be easily offset by modestly increased efficiency and drag reduction not to mention that a less fatigued skipper might end up being a better skipper when at the helm for extended periods in these conditions further compensating for slightly increased weight...
And finally you said: >> The empty well will create turbulence.
I'd have to agree... except in my original post I said: >> you could use "rubber slats" to automatically seal the bottom of the unused CB trunks to keep flow non-turbulent there as they do on retractable CB windsurf boards
I don't know if you're familiar with this approach but it works very well - two thin but tough sheets of rubber running along the length of the centerboard well, each attached along the outside edge as well as fore and aft, "kissing" in the midline. When the board is pushed down, the rubber parts and allows free sliding (also gives just the right amount of friction to hold the board where you want it) but when the board is raised, the slats close and present a very flush surface to the water minimizing any turbulence.
