Re fueling....I was in visioning shaft leading up the two or three decks to the hangar then the normal lift could be used to lead to the deck and vies versa to bring in....
As for the design I'm still tweaking and altering things, I don't want to go to big I'm basing this on the RN of the 1980's don't forget.....
you cannot bring nuclear fuel through the hangar deck. you have to be able to reach directly in to the reactor (don't ask me how exactly it works, I am trying to find this out myself, but as much as described above I know for certain)
also, you are designing the RN's first nuclear surface ship. whatever you say, you are going big already.
seeing that the CVF were an all new design, I can't see why this would not be.