You can exclude uploading of Revit linked files to the vault server by manually adding a property called "ExcludeLinkedFiles" and setting this property to True/False in the ApplicationPreferences.xml file.
To configure this setting:
Close any Revit application.
Open ApplicationPreferences.xml file in a text editor. (Typically found at "<C:\Users(username)\AppData\Roaming\Autodesk\Revit 20xx Vault Addin>")
Add the following line under the Category "ApplicationOptions" with the desired value (true/false).
Relaunch the Revit application.