If the server is an upgrade from 2.5 then it will move the VMX file to the VMFS with the rest of the files for the VM.
From the online manual:
Upgrading ESX Server : Relocating Virtual Machines
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Relocating Virtual Machines
This operation moves the .vmx configuration file from the ESX Server host to the VMFS3 datastore. At the end of this operation, all virtual machine data and configuration files reside in one folder on the datastore.
To relocate virtual machines
1 Right-click the ESX Server host in the VI Client inventory, and choose Relocate VM files from the drop-down menu.
When the relocation is complete, a dialog box appears with the following message: “The virtual machine files for host have been relocated successfully.”
2 Click OK to dismiss the dialog box.