
From Veeam perspective, the issue is fully understood thanks to the verbose VDDK debug logs obtained from the affected customers. There's clearly the new method added to hot add logic in the latest version of VDDK 6.5 (which Update 3a brings with it). The new method makes a call to the Virtual Disk Service (VDS) of Microsoft Windows in a seemingly unoptimal manner: it queries each VM disk sequentially one by one, but also re-queries EVERY previously queried disk each time as it moves to query the next one. So the more disks the particular VM has, the exponentially longer the whole process takes. We shared all these findings with VMware Support.
The only unclear part is why these VDS queries, even if unoptimal, take very little time in most environments - but in some environments (28 to be precise) they take by an order of magnitude longer. For example, we're unable to reproduce the issue in our own test environments no matter what we do, including throwing huge load on every component.