Any way to ask Duplicati to delete backup versions that are empty?

which means only their data is uploaded. Unchanged files refer back to previously uploaded data.

What happened to the unchanged files? If you purged only the rapid changers, the others remain.
Did you mean you think you have many backup versions where remaining files have no changes?
upload-unchanged-backups is how one can actually request that. You get a dlist and DB clutter.

is already some clutter, but sometimes it’s what people want. If not, adjust the Retention settings.
For example, if thinning out backups as they age is interesting, the no-changes-here ones age out because everything ages out. CrashPlan has that, but handles deleted files specially (unlike here).

Smart backup retention and Custom backup retention are the options for thinning with age. Looking forward, the backup runs which find no changes will just not make versions, unless asked. Attempting to get to that point retroactively may be hard, and it’s questionable what it will gain you.

EDIT:

Compact would probably be the wrong place, as its job is repackaging dblock files that grow empty.
The COMPACT command gets into this a bit, showing how one can tune the levels for when to run.

For one that’s probably worse than The COMPARE command, there’s the database and expert SQL.
FilesetEntry table where a FilesetID has the same set of FileID rows as another is a duplicate.
I think. This is probably the sort of comparision that the compare command uses to version-compare.