I work with Netapp but I am not directly familiar with Snapmanager for Exchange so hopefully somebody with direct experience w/ SME and virtualized Exchange can offer better insight. Likewise, apologies if this is just a total rehash of what you've investigated so far. I did a quick look for some documentation that specifically deals with this and I didn't find anything explicit. There are references to physical and virtual resources in the Snapmanager for Exchange admin guide but I believe those are related to Exchange cluster resources and not virtual disks or virtual machines.
Thinking it through, it makes sense that SME requires LUNs rather than vmdks if you take into account what it would be snapshotting. Leveraging an array snapshot against a vmdk is kind of tricky since the disk in question is actually a file sitting in a datastore which is in turn sitting in some pool of array-based storage. To get a proper snap of the filesystem inside the vmdk file, VMware snapshotting would be required. To make this VMware snapshot useful at the array level, there'd need to be some coordination between VMware and the storage array so that a 2nd snapshot (a storage-based snap) actually captures the vmdk filesystem in a state worth snapshotting (buffers flushes, ops quiesced, etc. by the first VMware snapshot). Additionally, since Netapp snapshots are volume-based, to get a snapshot of a vmdk, the entire volume housing the VMware datastore that the vmdk is in would need to be array-snapshotted and you can't easily "drill down" and just snap that part of the volume where the vmdk lives or pluck it out after the whole-hog array snapshot has been taken.
Snapmanager for Virtual Infrastructure does some coordination between VMware snapshots and Netapp array snapshots to streamline all of this but I don't know that Snapmanager for Exchange has that awareness.
SME Admin guide:
http://now.netapp.com/NOW/knowledge/docs/SnapManager/relsme50/pdfs/admin.pdf (NOW login required)