The reason for the double declaration is the additional 

<inherited>false</inherited>

setting in the second. The second part is only executed by the parent pom. The 
first part is executed for all the modules. Removing either might cause loss of 
javadoc. So we need to test if a full, and partial build will still create the 
correct javadocs before we remove anything.

There are actually three declarations of this plug-in in the file.  I think I 
got my line numbers messed up in the original post, but what I meant was this...

The first declaration is fine; but below that is this:

        <plugins>
            <plugin>
                <artifactId>maven-javadoc-plugin</artifactId>
            </plugin>
            <!-- seperate execution for parent aggregation of javadoc, not inherited by modules -->
            <plugin>
                <artifactId>maven-javadoc-plugin</artifactId>
                <inherited>false</inherited>
                <executions>
                    <execution>
                        <id>javadoc-parent</id>
                        <phase>site</phase>
                        <goals>
                            <goal>aggregate</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>

It's the second that seems spurious and is causing a warning.  The third 
(containing the inherited=false) is fine.

Fixed in r2310