Even using BTreeFolder to store all objects I was getting >300s delay to show a single object (ok, it's an archetypes-based one, containing >50 fields, splitted into 7 schematas, with lots of fancy stuff...). So I made a directory hash structure based on UID from each object (an AT UID is md5, so we have a hex base).
My own experience with BTreeFolder2 does not support your diagnosis. I do not believe BTreeFolder2 is the problem here.
On a CMF-based CMS that I helped develop the largest BTreeFolder2-based containers held ca. 60,000 items at the top level, meaning we did not use a directory structure to restrict the number of items per folder. There was zero delay retrieving singe items and even stepping into the ZMI where it shows 1000 ids at a time was sub-2 second response time.
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