Don't forget about the VM's memory swap file here. Unless you reserve all memory for a VM, ESXi will create a memory swap file for each powered-on VM in case memory needs to be swapped to disk. This swap file is equal to the VMs total memory size and is not counted as VM virtual disk space. So if you allocate about 1TB of memory to all your VMs, these swap files will occupy an additional 1TB of disk space on the datastore.
There could also be files lying around on the datastores, stuff like ISO files or VM files that were never properly deleted (e.g. VMs just unregistered from the vCenter inventory instead of deleted from disk).