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This is the answer that we received from Alfresco support when we asked the same question(s):
"This is a very old setting that for some reason still persists in our repository.properties files even up to our newest versions. However, the responsible context file that handles it is /root/projects/repository/config/alfresco/audit-services-context.xml. I believe the last time this context file had any pointers to it was in our 3.3.5 version.
To complete the answer for you though, the auditcontentstore and auditcontentstore.deleted folders were created when auditing was enabled. The auditing content was placed therein. The functionality was actually removed before 3.4.x. If you use audit now, it won't make use of this folder."
