The Novena has abundance of documentation, but its mass is overwhelming and it is hard to understand without electronic engineering knowledge, for instance this schematic. So I find myself unable to extract the information to answer my question, although it is probably hidden in this documentation.
The official website containing the documentation can be found here. It seems that they have not made official documentation yet.
The article you linked to, is over a year and a half old. Since then numerous other articles have been released saying it is now fully open source:
So to answer your question:
The entire laptop is open source - with one exception to this being the processor (a Cortex A9 CPU).