since each and ejb-jar is a collection of beans which contains an ejb-jar.xml to describe the beans, and an ear is potentially a collection of 0-n ejb-jar's and 0-n war's, then yes, an ear may contain mulitple ejb-jar.xml files.
you can put all your message beans in one ejb-jar, with it's own ejb-jar.xml, all your entity beans/session facade beans into another ejb-jar with it's own ejb-jar.xml, then you'll have multiple ejb-jar.xml files into one ear.
a single ejb-jar file though (a jar file that contains enterprise
java beans) can only contain one ejb-jar.xml. though it does not need to contain a META-INF/MANIFEST.MF file.