Does "Secure Empty Trash" securely delete the hidden version files for documents in the Trash in OS X Lion?
I just tested this out, and it appears that the older files do indeed get deleted. It did not matter if I chose Secure Empty Trash or simply emptied the trash normally, they were also deleted.

A little more detail:

To test this, I enabled the root user to allow me to peer into /.DocumentRevisions-V100 and the files within. The exact structure of this folder and its contents are better explained over in John Siracusa's Lion review (Internals, Document Revisions).

I created a couple files, then made some changes, saving new versions. The folder that contained the revisions populated with new files as I saved new versions. Within this top level folder, there's a folder called PerUID, which houses subfolders for each user account. Each user account folder contains a series of numbered folders, one folder for each file that has revisions saved. Thus, the actual revisions are saved as files a few levels down in this hierarchy, with hashed filenames. Emptying the trash (either way) would delete these files, but the preceding folder structure would remain in place.

Before deleting:
/.DocumentRevisions-V100/PerUID/0/5/com.apple.revisions
This folder still has the previous versions contained within.

After deleting:
/.DocumentRevisions-V100/PerUID/0/5/com.apple.revisions
This folder still exists, but it is empty.

I did not inspect the other folders within /.DocumentRevisions-V100/, so I did not check the databases that are contained within them. Siracusa goes into more detail, but they seem to exist to contain databases to track changes and map the user's files to the revisions saved by the system. I'm fairly certain that no document contents are saved there, though I'm not sure about filenames, and if filenames are present, if they're hashed or not.