Invisible website issue!

Hi guys

We are struggling to work out what is happening with one of our Joomla sites. Site auditor won't run and it seems the site has been all but de-indexed by Google. We get a "Not Fully Crawlable: 12 disallow rules" message in Raven Tools under Preparedness.

Can anyone give us a clue as to what might be blocking the site from being crawled or where we would find the disallow files?

We believe the site has been hacked at some point, so the files could be hidden away somewhere.

Any assistance or ideas welcome.

thanks