The truth is, any server CAN be compromised, no sane person would claim that there are absolutely no problems with any http/php code, certainly there are possible dialplan intrusions.
A good suite of security tools should include all the standard things plus a root kit tool, I use
http://rkhunter.sourceforge.net/
It would detect new files appearing in standard ( or custom) places which seems to cover the last few FPBX patches.
Watching for unusual calling patterns also, many attempted attacks happen early on Sunday morning 