When dealing with 100+ virtual machine, I usually use the IBM Spectrum Protect for Virtual Environment, which address your business needs using Tags instead of Folder.
Regarding the VDP support for Folder, it supports, but only Host and Clusters folder, not virtual machine folder, see: vSphere Data Protection and vCenter Server Folders - VMware vSphere Blog
The blog post I mentioned is quite old, but there is another one which even on the version 6, there still no support for virtual machine folders or tags, see the comments: What's New with vSphere Data Protection 6.0 and vSphere Replication 6.0 - Virtual Blocks
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Richardson Porto
Senior Infrastructure Specialist
LinkedIn: http://linkedin.com/in/richardsonporto