You can add the following configuration so that the contents of the .schema files from all the jars get appended together.
<configuration>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
<resource>META-INF/spring.handlers</resource>
</transformer>
<transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
<resource>META-INF/spring.schemas</resource>
</transformer>
</transformers>
</configuration>