Petr, i have already tried a similar boss-deployment-structure.xml (just for testing purposes) like yours, but in my case i got the jboss hibernate libs completely excluded from my ear classloader, and started to get classnotfound exceptions since i have a JPA layer. Then i tried adding the exclusions to my war deployment and their were still visible... seems like the oposite result from what you got.
ps: Using jboss7 cr1