Looks like they haven't added that functionality in the free FastSCP. But the paid for Backup and Replication, leaves you with a compressed Veeam backup file (.vbk) which will be equal to, and in most cases a lot less than the size of the volume of data actually stored in the .vmdk. It depends exactly what functionality you want out of these backups. The client allows for you to mount any VMs disk in the .vbk file in seconds and you will see the full folder structure at which point you can copy any files you want to restore out. Or restore the whole virtual machine back into the environment.
Maybe take a look at the ghetto scripts:
http://communities.vmware.com/docs/DOC-8760
These are a free alternative and it looks like they output in a variety of formats including thin. Not tried them myself but they are quite popular.
Hope this helps,
Dan