To weigh in, I find that stone count (and I'm only saying stone instead of all loose items because it's easier to track) doesn't have a noticeable effect until you're in excess of 5k stone, and doesn't start to really slow down your fort until 10k-15k. However, loose items get more of a bad rap than they're due, FPS-wise. The main things that kill FPS are mass designations, fluid motion, inefficient pathing (and most people will never notice the first).
I'm not sure if this has been brought up in the thread as I kind of skimmed it, but building floors and what not out of stone does increase your FPS, albeit by an incredibly tiny and insignificant fraction. My reasoning is thus: terrain is procedurally generated via various codes and biome information; data is not necessarily always tracked. This is why pouring desalinated water past the z-level of a salt-water aquifer (with the aquifer being contained and not contacting the fresh water) will result in magically salinated water, and why casting obsidian in a soil layer, then building a floor on it and deconstructing it will result in a soil floor. The game knows what z-level of what biome ought to be salt water and what z-level of what biome ought to be what stone/soil type. So if you have a regular microcline cavern floor and build a felsite floor on it using a loose stone, the game is suddenly tracking one less bit of data: Before you build it, the game is tracking biome information, that specific tile's information (natural, microcline, unsmoothed, unengraved, no liquids, etc), and the stone unit. Afterwards, it is only tracking biome information and the tile information - it is no longer tracking that the floor was a microcline floor. Upon deconstructing the felsite floor, a new microcline floor is created and tracked via biome information, much like the soil-on-cast-obsidian thing. Just a theory, but one I have a lot of confidence in. When you wipe items from your game (chasming, proper boiling, atom-smashing) FPS does increase, but not enough that anything you can do without editing the raws will cause a noticeable impact. If you have a fort of 100 dwarves hauling stone to the magma sea for a year nonstop, they'll probably only clear a few thousand stone, which probably won't really make a difference to your FPS at all, and frankly, isn't worth the damn time, whereas if you're not above it, you can edit all the [layer stone] to boil into a pleasant mist, forward your game one frame, then remove the appropriate tags, eliminating a few hundred thousand stone in one go and throwing on 10-40 FPS depending on your fort. The best non-raw-editing thing you can do about stone is just avoid purposeless digging. Your average fort isn't going to generate enough stone to run down the processor unless you're doing something radical. And if you take the time to pave areas down with the stone you dig, it'll probably help slightly in the long run.
Outside of item tracking, the best things you can do for FPS are to keep efficiency very high (and use traffic orders) and try and get fluids to even out - an area of completely motionless 3/7 is just as lagless as a full 7/7 area, so a keenly-observed bucket brigade can balance most things out. Also, if you're not megaprojecting or building a massive military, there's no harm in culling migrants before they befriend anyone.
God, I hope this post made sense. I think I rambled on a bit there.