Need a Document Organization Tip

My current project involves upwards of nearly 1,000 documents. One folder alone contains 592 documents and folders. I’m curious as to whether it would be more efficient to have more folders with fewer documents in each folder than to have fewer folders with large numbers of documents? Or, does it even matter? (The only issue I’ve noticed using the current binder tree configuration is that large folders understandably take longer to respond when viewing the folder scrivenings. There is one exception, however. On the folder with 592 documents, when I click on that folder and it finally comes up with the scrivenings view, if I try to change the name of the main folder, Scrivener crashes and closes. But when I open the program again everything seems to have been saved – including the new name of the folder.)