One of my ESXi 6 hosts had the configuration issue message stating: “Deprecated VMFS volume(s) found on the host. please consider upgrading volume(s) to the latest version“. I only have two LUNs presented to my hosts and both are VMFS5:

After some brief searching I found VMware KB article 2109735 which states the possible cause:
This issue occurs because at the time of initial detection, the version of the filesystem is not known. Therefore, comparing it against the list of valid filesystems does not return a match.
Looking through the hostd log I did find the entry mentioned in the KB article. It appears that after I renamed my StarWind LUN it did not report the filesystem to the host fast enough which caused the error to occur:
/var/log/hostd.log

The resolution was to restart the management agents on the host. I put the host in maintenance mode then restarted the management agents:
services.sh restart

After the management services restarted the error cleared:

Leave comments below if you received this message and this KB article resolved your issue!
KB2109735:
http://kb.vmware.com/selfservice/microsites/search.do?language=en_US&cmd=displayKC&externalId=2109735&src=vmw_so_vex_sbori_1079