From Mule's parent POM:
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.9</version>
</dependency>
So yes, Mule relies on JUnit 4.9, whether you depend on it directly or not.
When you add:
<dependency>
<groupId>org.mule.tests</groupId>
<artifactId>mule-tests-functional</artifactId>
<version>3.3.1</version>
<scope>test</scope>
</dependency>
to your project's POM, JUnit 4.9 should be pulled in for you.