With regards to webappDirectory the default project layout with Maven for a WAR is to have src/main/webapp/WEB-INF/lib with src/main/webapp being your top level directory. The WebContent/ is an ECLIPSEism. Now it woule be good if the Maven plugin for Eclipse (m2e) could relocate (virtually) and link the src/main/webapp tree back at the top level of the project for easy access, like Java Source folders do.
So if you are messing with the webappDirectory setting (by removing it) in maven-war-plugin then be aware of the defaults.