"This is because some developers did not declare that their app client modules depended on EJB JARs"
Did not? Or did?
You mean that if such a dependency would be declare, those ejb jars would not appear anymore in the returned client jar?
How do they declare such dependence of an application client module to an EJB jar? In application-client.xml schema i don't see nothing related.
Anyway, in my ear I don't have any app client module, so no point in having the EJB Jar or any of its utility jar ear-dependencies (listed in ejb jar's manifest.mf file).
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