I think what a lot of people do in 34.11 is make pairs of stockpiles. This is what I do for meat/plants/armor/weapons/clothes/leather/cloth or really anything that ends up being heavy in a bin: make two stockpiles, right next to each other. One is maybe 5x2 and DOES NOT accept bins. The other one, probably larger, is right next to it and accepts from links only and takes from the original and DOES allow bins (or barrels). This way, when a dwarf picks up a bin to stuff an item into it, he is only traveling a couple tiles instead of halfway across your fort.
This keeps dwarves from hauling bins to the surface and otherwise spending days at a time carrying heavy-ass bins. You said dwarves "refuse to retrieve items from bins" and I don't think I've had this problem. It is true that is you modify a stockpile, the "removed" items do not get drawn from "mixed" bins but this is rectified by just making your stockpiles hold what you want the first time you make them. (IE don't make a stockpile that holds all finished goods and weapons and armor at the beginning no matter how tempting...)
Large spaces that are mined out but aren't going to be used should be sealed off or marked with traffic designations. But, if you are going to use the space for something, then there's no need to stress about the FPS loss. I think it will be marginal anyway. I am by no means an authority on the issue, but I remember spending an afternoon trying to boost my FPS in a large fort with about 200 population. I felt like time spent messing with pathing and traffic designations yielded very little (if any) change in FPS. However, there are many other things which can and will raise your FPS: lowering G_FPS, turning off weather and/or temperature, destroying excess stone, destroying/trading useless items, and slaughtering/caging large numbers of livestock. Personally, I never saw ANY change in my FPS by changing traffic designations. That's just me, though. Certainly do not worry about 2-tile wide hallways.
You said something about letting items pile up in workshops. This is fine, to a degree, but workshops WILL become cluttered and this has an impact on how quickly items will be completed in that workshop. Just a warning.
Quantum stockpiling with minecarts is awesome, and pretty easy once you get the basics of setting up a route. Follow the guide on the wiki and you will have it down in no time.