From efficiency point of view, I was bigger about cube forts 'till I realized that stockpile to workshop dominates the calcs.
I play at 20 FPS *on purpose* and my forts rarely last longer than 10 years (because I get interested in doing something else), so I've never even come close to FPS death. However, I continue to believe that this is the dominant issue for both efficiency and FPS. Path finding is dramatically computationally easier when the paths are short. If you have stockpiles 2 tiles from the workshops, then virtually nothing matters when the dwarf is pathing from the stockpile to the workshop.
But then you have to consider the path the dwarf will take to get to the stockpile. The key is to keep everything that the dwarf is likely to want in a small enough space that their paths remain short. Now, it's hard to do this, admittedly. But if you think of your work flows, it really helps. Have a food stockpile near your farms. Possibly keep staging stockpiles near that, to split up hauling jobs if the paths are long. Keep your still near the farms (so that the seeds don't have to go very far). Keep a bag stockpile nearby for the seeds. Consider only enabling hauling for certain dwarfs -- so food industry dwarfs haul food, but nobody else does.
However, also consider having many small shrines and temples so that a dwarf has an option to pray near where they work and live. Don't centralise the housings. Allow dwarfs to live near their workshops. The list goes on. Basically, the shorter the paths, the better off you are going to be. I hear people talk about their dwarfs hauling things for a week, and then complain about FPS. It's much better to split up the hauling so each dwarf only hauls something for no more than half a day (say 50 tiles at full speed, much less if hauling heavy things).
The real difficulty, though, is when a dwarf decides to go to the tavern at the surface and then has to go back to work in the magma forges. There isn't much you can do about that, but at least you can design the fortress so that it isn't *required* to do that kind of thing.
I also think that this kind of fortress looks a lot more interesting and "real". It's also super challenging to do, which I enjoy.