I'm not sure when it was introduced, but there's now a low-level property in Preferences to enable this feature.

1. Open Preferences
2. Click on the Low-Level Properties category
3. Click the I accept the risk! button to open the Low-Level Properties panel
4. Enter "empty" in the search filter to locate the feature
5. Double-click the "commit.allowToCreateEmpty" key to edit its value
6. Select the true radio option and click the OK button
7. Click OK to close Preferences panel

You should now be able to select a workspace in SmartGit and click Commit... from the context menu to create an empty commit.