... actually files in Briefcase are being stored the same way like E-Mail Messages:
Metadata like Filename, Size etc. is being stored in the MySQL Database. To be precise in the "mail_item" table of each mboxgroup# Database. The table columns "sender" and "subject" contain the filename in cleartext.
The file itself is being stored like all other E-Mails somewhere in one of the message store directories.
Depending on HSM and Message store settings it may be compressed or hard-linked as well. So it isn't possible to retrieve a file stored in a Briefcase by just finding it somewhere on your disk. If you really want to know in which file on the disk a briefcase document is being stored there's a great Wiki article by AJ Cody explaining the details:
Ajcody-Mysql-Topics - Zimbra :: Wiki
I would recommend to use the REST API:
ZCS 6.0:Zimbra REST API Reference:Get Briefcase - Zimbra :: Wiki
To download your entire Briefcase as single ZIP file you can use your Browser or a command line utility like wget or curl:
http://localhost:7070/home/john.doe/Briefcase?fmt=zip