Ok i got it working somehow.
First thing - mistake in jboss-deployments-structure.xml module name should start with deployment. so correct is:
<module name="deployment.my-app.ear" export="TRUE"/>
<module name="deployment.my-app.ear.ejb1.jar" export="TRUE"/>
Second - When injecting ejb I have to use @EJB(lookup=GLOBAL_JNDI_NAME) with that jndi path which sucks but I can live with that. Without path it throws WFLYEJB0406 and @Inject annotation throws WELD-001408.
If someone knows about some kind of idea how to realize idea about plugin system in Wildfly(or generally JEE) please post it here thanks.
I'm facing a very similar problem and also have to use the GLOBAL_JNDI_NAME.
Did your or somebody else found a way to avoid the setting of a lookup name?