You simple need to copy the generated pdf/rtf/html whatever to the correct location and it will be deployed with the maven-site or you can generate directly into the target location for the site like this:
<plugin>
<groupId>com.agilejava.docbkx</groupId>
<artifactId>docbkx-maven-plugin</artifactId>
<version>2.0.14</version>
<dependencies>
<dependency>
<groupId>docbook</groupId>
<artifactId>docbook-xml</artifactId>
<version>4.4</version>
</dependency>
</dependencies>
<executions>
<execution>
<goals>
<goal>generate-pdf</goal>
</goals>
<phase>pre-site</phase>
<configuration>
<sourceDirectory>${basedir}/src/docbkx</sourceDirectory>
<xincludeSupported>true</xincludeSupported>
<includes>maui.xml</includes>
<foCustomization>src/docbkx/fopdf.xsl</foCustomization>
<targetDirectory>${project.build.directory}/site/</targetDirectory>
</configuration>
</execution>
</executions>
</plugin>
You shouldn't use site:deploy you should use mvn site and mvn site-deploy instead to get run the site life-cycle.