Let me tell you about a fortress I had once. I had dug out two 3x3 up/down staircases that penetrated all the way to the bottom z-level of the delve, and then I made five-space wide corridors coming out in all four cardinal directions from these, going all the way to the edges of the map. The result was that they would intersect in two places, and I ended up with more ore than I could process for a very long time, which was neat.
The problem was that at a certain point during mining, the game got unbearably lagged, so I cleared out three of the 15+ z-levels of worthless stone I had by dumping it into my rock crusher, a small drawbridge with a garbage dump activity zone under it, linked to a lever for instant destruction of crap I didn't want.
After all the dumping and crushing of these three z-levels, I still didn't have a very good framerate, and so I figured maybe it was because the dwarves and other creatures were running pathfinding checks on all the mined squares, as out-of-the-way as they were. So I walled them off, but left a space for a door on each of the four walls of my up/down staircases, which I locked when they were built.
FPS got a lot better, but apparently I mined too close to the edge of the map, and to my very tragic chagrin, goblin thieves and, eventually a siege full of bowmen, spawned in the open areas underneath my fortress, to plunder and slay with near total impunity before I could check them, which was only possible by taking enormous losses of military and civilian dwarves.
So I took out all the doors and just walled everything off. Ran a lot better after that, and no nasty surprises.
Oh yeah, I almost forgot another problem with FPS that made a big difference. I had a volcano in that fortress, and while heat wasn't slowing down my FPS noticeably before all that mining, it was also a cause of a big chunk of my problems. A friend explained that heat flow takes up a lot of cycles, just like water and magma flow.