If a sub deployment uses another sub deployment's module-alias as a dependency, it will deploy successfully, but if hot deployed, it will fail with the error below. Attached reproducer.
<?xml version="1.0" encoding="UTF-8"?>
<jboss-deployment-structure xmlns="urn:jboss:deployment-structure:1.1">
    <ear-subdeployments-isolated>true</ear-subdeployments-isolated>
    <sub-deployment name="ejb1.jar">
        <module-alias name="deployment.ejb1"/>
    </sub-deployment>
    <sub-deployment name="ejb2.jar">
        <dependencies>
<!-- works
            <module name="deployment.test.ear.ejb1.jar" slot="main"/>
-->
<!-- fails with  WELD-001408: Unsatisfied dependencies for type TestEJB1 with qualifiers @Default on redeploy / hot deploy -->
            <module name="deployment.ejb1" slot="main"/>
        </dependencies>
    </sub-deployment>
</jboss-deployment-structure>


10:59:16,284 ERROR [org.jboss.msc.service.fail] (MSC service thread 1-3) MSC000001: Failed to start service jboss.deployment.unit."test.ear".WeldStartService: org.jboss.msc.service.StartException in service jboss.deployment.unit."test.ear".WeldStartService: Failed to start service
	at org.jboss.msc.service.ServiceControllerImpl$StartTask.run(ServiceControllerImpl.java:1936) [jboss-msc-1.1.5.Final-redhat-1.jar:1.1.5.Final-redhat-1]
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [rt.jar:1.8.0_60]
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [rt.jar:1.8.0_60]
	at java.lang.Thread.run(Thread.java:745) [rt.jar:1.8.0_60]
Caused by: org.jboss.weld.exceptions.DeploymentException: WELD-001408 Unsatisfied dependencies for type [TestEJB1] with qualifiers [@Default] at injection point [[field] @Inject private test.TestEJB2.test1]
	at org.jboss.weld.bootstrap.Validator.validateInjectionPoint(Validator.java:315)
	at org.jboss.weld.bootstrap.Validator.validateInjectionPoint(Validator.java:284)
	at org.jboss.weld.bootstrap.Validator.validateBean(Validator.java:147)
	at org.jboss.weld.bootstrap.Validator.validateRIBean(Validator.java:167)
	at org.jboss.weld.bootstrap.Validator.validateBeans(Validator.java:386)
	at org.jboss.weld.bootstrap.Validator.validateDeployment(Validator.java:371)
	at org.jboss.weld.bootstrap.WeldBootstrap.validateBeans(WeldBootstrap.java:379)
	at org.jboss.as.weld.WeldStartService.start(WeldStartService.java:65)
	at org.jboss.msc.service.ServiceControllerImpl$StartTask.startService(ServiceControllerImpl.java:1980) [jboss-msc-1.1.5.Final-redhat-1.jar:1.1.5.Final-redhat-1]
	at org.jboss.msc.service.ServiceControllerImpl$StartTask.run(ServiceControllerImpl.java:1913) [jboss-msc-1.1.5.Final-redhat-1.jar:1.1.5.Final-redhat-1]
	... 3 more


Note if you just undeploy instead of hot deploy this NPE happens, which could be related

10:59:49,103 ERROR [org.jboss.msc.service] (MSC service thread 1-2) MSC000002: Invocation of listener "org.jboss.as.server.moduleservice.ServiceModuleLoader$ModuleSpecLoadListener@4806eb9e" failed: java.lang.NullPointerException
	at org.jboss.modules.ModuleLoader$FutureModule.access$400(ModuleLoader.java:645) [jboss-modules.jar:1.3.7.Final-redhat-1]
	at org.jboss.modules.ModuleLoader.unloadModuleLocal(ModuleLoader.java:435) [jboss-modules.jar:1.3.7.Final-redhat-1]
	at org.jboss.as.server.moduleservice.ServiceModuleLoader.access$200(ServiceModuleLoader.java:58) [jboss-as-server-7.5.7.Final-redhat-3.jar:7.5.7.Final-redhat-3]
	at org.jboss.as.server.moduleservice.ServiceModuleLoader$ModuleSpecLoadListener.transition(ServiceModuleLoader.java:105) [jboss-as-server-7.5.7.Final-redhat-3.jar:7.5.7.Final-redhat-3]
	at org.jboss.msc.service.ServiceControllerImpl.invokeListener(ServiceControllerImpl.java:1565) [jboss-msc-1.1.5.Final-redhat-1.jar:1.1.5.Final-redhat-1]
	at org.jboss.msc.service.ServiceControllerImpl.access$2800(ServiceControllerImpl.java:52) [jboss-msc-1.1.5.Final-redhat-1.jar:1.1.5.Final-redhat-1]
	at org.jboss.msc.service.ServiceControllerImpl$ListenerTask.run(ServiceControllerImpl.java:2131) [jboss-msc-1.1.5.Final-redhat-1.jar:1.1.5.Final-redhat-1]
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [rt.jar:1.8.0_60]
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [rt.jar:1.8.0_60]
	at java.lang.Thread.run(Thread.java:745) [rt.jar:1.8.0_60]