Hi,
I am using Tetra4D Converter to manage my 3DPDF conversion. It allows me to convert some of my CAD files with only graphical information that allows to my sales and my marketing dept. to handle my models in Acrobat, without any geometrical information. Like this, if my sales team want to get a quote to a subcontractor, no problem, it will be not possible for them to export the CAD dat and use it.
But you can decide to convert the geometries, in some cases it could help. This is just up to you...
For the Acrobat security, it depends of what you want to do...More info here:
Acrobat Help | Security
Hope it will help you....