Some things that I didn't see mentioned:
• Vast majority of efficiency improvement in layout is in how close your raw materials are to the workshop. You already know how to qsp everything into 1 pile in a general area.
I've written more lengthier post on this recently:
1 2 • I don't see any minecart on the penultimate level for the stone qsp, and it looks like your large pile two zs above has barrels/pots in it.
So, I'd suggest to check that dwarves aren't in a hauling loop with those qsps.
• Your large bathtub has ring of blood. If you drained it once to map edge so that all tiles have at least 1/7 when resealing the floodgates, you'd estabilish a permaflow that would wash all the blood into the walls/floors/floodgates on lowest level, keeping where your dwarves walk clean.
• Pathing over creatures forces detours and drains fps. Just checking that your turkeys in 6th sublevel are in cages and not in the way of dwarves?
• For booze, automation wasn't mentioned. Back in 2015, there was workflow, and nowadays there's also manager update in 0.43. Either would let you keep a constant level of booze handy, with new jobs whenever booze dropped below a level you can decide.
• For providing happy thoughts, being within 1 tile of building to admire works.
I generally put stockpiles on stair or ramp tiles, but if you're not doing that you can instead put furniture or bridges there (though bridges on stairs need to be retracted to allow passage).
Dwarves especially like their own buildings (x2), that are 'tastefully arranged' in statue garden (x2), made from materials they like (x2) [all stacking].
Though note that dance floors in new taverns cannot have anything on it.
• Ballista boast great range, but they're generally not effective as standalone compared to newer options, tending to cause bruises only if you're not a tree. Setups of them tend to favour making the targets dodge into some flavour of doom.
Though here in particular the arrow stockpile is more tiles away from the ballista than the goblin has to walk to get in range of scaring the civilian away (even ignoring the crawling speed of hauling an arrow), so they can likely fire only once.
I'd suggest repurposing the room as minecart grinder, drowning trap (with some buildingdestroyer trap somewhere to deal with singular non-drowning creatures), or even just plain "lock the doors when inside, drop them down and peck to death with bolts".
• To secure hospital against werebeasts, you'd ideally need a multi-level one so that emergency rooms are accessed from above and lockable with hatches - as when one cannot path to hatch's z-level one cannot break it.
• Your fort's a little split between above and below aquifer. Well, once you've broken through once, it is much easier to make a bigger breakthrough for the aquifer with map edge draining to below.
Also, if you muddy stone tiles, you can place farm plots there, allowing you to bring the farms bit closer to the fort.
• Might want to add some magma for magma workshops.
• Also, with 100 dwarves could very well do a cross-training program, putting everyone in military rotation. The increased stats alone make this worthwhile, plus now it also satisfies needs and gives happy thoughts for improvement of a skill.
If you give them armor, you'll also get rid of most clothing needs, though note that metal armor slows raw recruits without any armor user.