I seems to be a kind of a bug. After some more testing, I discovered that if I remove all wb-resources from the above file, nothing gets deployed. E.g.:

<?xml version="1.0" encoding="UTF-8"?>
<project-modules id="moduleCoreId" project-version="1.5.0">
    <wb-module deploy-name="foo_main_ejb">             
    </wb-module>
</project-modules>

This will cause an empty deployment for the EJB module. However, if I put only one random (but existing) entry here, all source directories will be deployed. E.g.:

<?xml version="1.0" encoding="UTF-8"?>
<project-modules id="moduleCoreId" project-version="1.5.0">
    <wb-module deploy-name="foo_main_ejb">        
        <wb-resource deploy-path="/" source-path="/resources"/>        
    </wb-module>
</project-modules>

This will also cause the previous shown /src to be deployed as well as any /test /resources /foo /bar /whatever source dirs I have in the EJB module. If I put a reference to a non existing directory in the source-path (e.g. /does_not_exist) then nothing will be deployed, so there seems to be some level of validation being done before it decides to deploy everything there is to deploy.

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.