This little gem above is a bug that is included in your ESXi version 6.0 update 1. While it’s a pain to fix it is pretty easy solution and doesn’t actually mean you have deprecated VMFS volumes on your host. But just to make sure check anyway and make sure this bug applies to you.
The solution is pretty simple by restarting two management agents on each affected ESXi the error will clear, of course until you add a new datastore. Then chances are the error will reappear. If you have a massive amount of ESXi hosts and the option is available to update to ESXi 6.0U2 then I personally would update instead of restarting these agents on all your hosts.
Step 1: Log into your ESXi host via SSH or DCUI
Step 2: Run the following command to restart the management agents on the box
This command will reset the management agents on the ESXi host and clear the deprecated VMFS tag that has plagued your vcenter.
Kb article is below for more from VMware.
VMFS deprecated datastore 2109735