I did the same installation and it works fine in geonode2.6.3. It´s important that you edit the file in the correct path: /home/geonode/geonode/geonode/templates/site_index.html (or whatever name you put to your project instead of "geonode").
Also check your wsgi.py file, that it´s pointing to your geonode project:
NOTE: by only changing back to "geonode.settings" in this file you can change the whole theme from your-project-theme to the default one.
It is not necessary to restart apache to see this changes, but depending on your browser you might have to empty cache.
If you edited the css files, run the collectstatic command to see changes.
All template files you want to edit, should be copied first to the above path in the same location they are in /etc/geonode/templates. For example: if you want to edit the layer_details.html file, wich is in /etc/geonode/templates/layers/, copy the file to /home/geonode/geonode/geonode/templates/layers/layer_detail.html and edit this one (it´ll override the first one). You can edit straight in the /etc/geonode but you will have a better organized geonode project if you work on your geonode project folder, and you also keep a backup 0km file if you ever need it.
Hope this helped.