I've been recently dealing with a similar dilemma. I've been starting to breed marmorkrebs. One dropped it's first batch a few weeks back with about 20 fry. I left 15 in the tank with the parent and only 2 have survived in there so far. I removed 1 and put in a $1 vase I bought at the dollar store with an airstone in there and is still alive. The other four I put in 2 1 gallon nano tanks I had already set up. All 4 have survived in those as well and both have airstones.
I think the most cost effective route while maintaing high survival would be to separate fry a few per tank/area. That being said I think you could very easily go out and buy a bunch of cheap tupaware 1g or bigger depending on budget. Buy an air pump and just use splitters and flow nobs and run a bunch of them together. Building a sump or canister filter will cost you way more than that would for the filter alone probably. Plus you have to deal with building, time, materials, risk of leaks, all crayfish on one system. Least with individual containers they can be isolated in they're own water column. Not that crayfish get diseases much but would def suck to loose them all to something rather than one or a few.
FYI I only change the water twice a month in those nano's so they are def tough buggers and can easily get away with being in a container with just an air stone. Better yet you could even buy small sponge filters if money permits.
75G, 29G, 20L, 12L, 10G, 5 Nano's, 3 Betta bowls
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*Everybody has too much of something...me? I have fish tanks.*