There were JBIDE-10318, JBIDE-9836 before. They were pretty strict in that deploying expoded JARs in WAR/WEB-INF/lib is not allowed for some reason. The only actual reason seemed to be that the server at the time refused to deploy such structure. Maybe the server was in the wrong? This was fixed in AS7-4704.
Now with Wildfly 8.2.0.Final exploded JARs in WAR/WEB-INF/lib deploy correctly, at least Weld, EJB, JSF seem to work fine.
The main use case for this is creating a modular web application, with different parts implemented in separate projects. Hot deploying of resources, such as Facelets' XHTMLs, is crucial for development. So the JARs need to be exploded.