Well, I've had the chance to try a few suggestions\ideas;-
1. The Ballista(s);- Hit and miss. I had to try this on the humans due to the dwarf caravan skipping the bridge and attempting a river crossing into some wildlife. I was hoping that targets would be slammed clear of the depot, but most dropped dead inside. Coupled with the inability to hit the broadside of a barn at point blank and the cost of munitions, I don't think it's really viable or fast enough.
2. Pumping the water out;- Items still move and go missing, I didn't notice any improvement over using a single drain. 1 marksdwarf did get washed through the fortifications+bars blocking the drainage channel and escaped somehow.
3. The air lure;- Too time sensitive, Urist Mcleverphobe needs to open access to the air chamber just as the water level reaches the drowning point. I did have some success opening the air chamber in advance and using the waterflow to shove the still living merchants&guards out of the depot. Some items were still in the depot, however that might be due to the 'Get out of my depot' system killing its target rather than just wounding it.
Unfortunately I can't attempt to freeze them in my current biome. I'll try that with my next embark.
Claim and dump isn't really in the spirit of it. I'm a fan of multipurpose traps really. Steel, flux, and hatred of the dwarvern leadership caste is the current motivation, but it never hurts to have something you can use on elves and humans too.
Washing them out of the depot into a side room\DAS seems to work well enough even with a 1x5 room (although size is less of an issue providing they finish under the DAS). It's just getting the water out. Maybe a fork shaped room along the lines of;
000000
X___B0
X_0000
X___B0
X_0000
X___B0
000000
X:Floodgates
0:Wall
_:Empty
B:Retractable bridge over a pit
If they're forced back over the pit, then I can dump them into 1x1 rooms to drain the water without any room for items to move into quantum space, then drop them again into a room containing the DAS. Resulting in 3 nice clean piles of items to pick through and no need for mass designating (and thus no hauling trash). If that works I could even scale it up, with stops added for the smelters, crypts, and stockpiles, before finally dumping everything that's left into the trash compactor.