In my experience, about the only time IDE deployment is used is to deploy to the developer's own "sandbox" environment. Any deployment to an integration test environment or to a production environment is usually done through an Ant script. The Ant script will usually check out the code from whatever SCM tool is being used, compile it, package it, and sometimes copy the EAR or WAR file to the receiving environment.
One of the problems with using WAR files created through an IDE is that the WAR file reflects only what was in that particular developer's work environment, not what was checked in to the SCM tool. With an Ant script, there is no question about the fact that the WAR file contains only what was actually checked in to the SCM tool.