This issue can be closed. The problem is fixed by using --phpunit-xml instead of --jdepend-xml to generate the PHP_Depend XML logfile.
However, this sounds broken to me as --phpunit-xml is likely to go away at some point. Back in 2007  I added functionality to PHPUnit to calculate, collect, and report software metrics. This was, of course, wrong. Half a year later  I removed that functionality from PHPUnit. At the time some people were relying on PHPUnit's XML logfile for these software metrics which is why Manuel Pichler added the --phpunit-xml argument (and respective logfile format) to PHP_Depend.
Long story short: pdepend + --jdepend-xml gives you a logfile that follows a de-facto standard while pdepend + --phpunit-xml gives you something that is deprecated.
Now if the logfile generated by --jdepend-xml does not contain all the information you need please have a look at --summary-xml. This is the actively maintained logfiles format of PHP_Depend.