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[Quietust]

However, THAT method leaves the creature's data in the creature vector, which still complicates memory access times for the structure.

Atom smashing them has been PROVEN to REMOVE them not only as an in-game annoyance, but to literally DELETE their entry in the creature vector table.

Kohaku and pals did extensive testing on this in .34.

Not quite enough testing, if that's the conclusion they reached...

Atom-smashing an item will delete it from the game entirely, though some "soft" references might remain (mainly for owned items and corpse pieces).

Atom-smashing a unit, on the other hand, just kills it - the dead unit will remain forever in the list of Dead Units, and that will potentially contribute toward lag (and also restrict the number of migrants you can receive). The only time units normally get removed from the Units list entirely is when they leave the map (and those tend to come back eventually), and possibly also during a retire/reclaim cycle (which can have its own problems), but there is a DFHack script "fix/dead-units" which will do what you're describing.

[Dorf and Dumb]

I think that there is one single pathing bug where things are trying to get through a locked door that overwhelms everything else on FPS.  I mean, I had a fort down to 10 and got it back up to 40+ by finishing the wall in one tile behind a door.  The bug seems to come when the critters that want in are in a REALLY big space, outside, HFS, caverns.  The long term solution, I think, is Pax Incarcerata - get enough sample critters from each locale walled/bridge-locked into little tiny spaces that no more are ever generated.  You can let your dwarves lounge around in bedrooms beside the glowing pit if you have the right critters locked up.