http://www.mhonarc.org/ is a perl script that will recurse though folders of emails, unpack the attachments and generate html versions of the mail, with links. A simple find can them delete the attachments, or you could just keep them as the result will be (mostly) smaller.

You are right to replace the software on the synology, as it uses a hacked ext2 filesystem which makes filenames case-insensitive (for windoze I suppose). This is a bummer for your nfs mounts from a unix system.