Note: this might go under improvement or new feature
Currently, so far, as documented and as an only option, Zabbix uses vfs.fs.size for reporting disk space in bytes.

In case when file handles/descriptors are open, but files deleted, this causes ESTIMATE reports about used space and looks like this is VFS layer-related. There must be more secure and trusted way for checking disk space usage.
(similar issue explained: http://www.cyberciti.biz/tips/freebsd-why-command-df-and-du-reports-different-output.html)