[Chris8]

But the thing that is essentially concerning me now the most here in this whole mess actually is:
Supposedly if they had access to write/modify files on vb.com and vb.org servers (By the way, isn't it the same server? Or Vb.com is on separate server from Vb.org?) are all downloadable scripts, mods, templates safe? I mean, assuming they had that access they could for example change certain mods or themes code to put vulnerabilities into them so they can hack other websites powered by vbulletin later.

So, ideally if vb staff knows they had such access vb staff should do the diff of all downloadable content against the backups from the time before it happened to make sure people are safe when downloading and installing new content on their forums/servers.
Also I would be more calm if they (you - I guess people in charge/responsible for vb here read this) could make a statement assuring your customers that everything is safe and nothing was modified or if there was anything modified that you took care to fix it.