I think I already found the way to make it work.
If I select "Allow output folders for source folders" in project properties -> Java Build Path -> Source, then the source folders as defined in "Deployment Assembly" seem to work.
If there thus is a bug, then it's that if source directories share an output folder (in many cases this will be the default output folder), it makes no sense to list them individually in the Deployment Assembly page. There could also be some explanation somewhere that mentions the functionality is working on the output folders perhaps.