I’m treating Cuba less as a Confederate state and more like the Arizona territory. The Union didnt take Cuba because they cut it off, but most Cubans opposed the Confederate territorial government, and the Confederates were unable to exert much direct control on the island.But if it rebelled and pledged itself to the Confederates wasn't it reconquered all the same by the Union? As a recent acquisition I'd think there'd have been some attempts at Cuban independence in the time as well with the USA in such chaos.
Even if Cubans revolted to restore independence, the Union would just have restored order post-war. Now that I think about it, I might include something like that in a future update.