To effectively troubleshoot and manage hundreds of VHDs there should be tooling to list contents to see why it's ballooning, check the startup and desktop folders, selectively delete certain parts, scan for white space then defrag the disk, repair corruption etc. Even when the user is actively using the VHD file. There are some elaborate homebrew Powershell scripts but nothing official.
Thank you for your feedback. We have a new tool in preview. We recommend you to have a look: https://docs.microsoft.com/en-us/azure/virtual-desktop/troubleshoot-azure-monitor
Have you tried the our portal integration for the latest release? Start here: https://aka.ms/wvdgetstarted