That's correct, if you want a full rename you would need to power the system off and rename all files including entries in the .vmx file OR if you have vCenter and sVMotion license, you can svMotion the VM and it'll rename the entire directory structure for you.
Regarding orphaned, I thought someone wrote a PowerCLI script to detect this but I don't recall, let me search around.
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William Lam
VMware vExpert 2009
VMware ESX/ESXi scripts and resources at:
VMware Code Central - Scripts/Sample code for Developers and Administrators
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