Are you absolutely sure it was a level 6 site? On a level 6 site, level 5 gets you access to security logs and cancel alert, and then you have to get another level of access to see the hidden files. There are definitely sites that just top out at level 5, which also get you security logs and cancel alert at level 5 but then don't have a further access level. I'd be very surprised if you didn't just encounter a level 5 site. If it's a genuine level 6, what did level 5 access get you? Nothing?
EDIT: Rather than speculate, I checked your adventure logs on Al's site. You gained level 1 access to Next Wave Advertising and Marketing with 28/100 energy left at 2010-03-02 17:19:18. You got full control with 24/100 energy left at 2010-03-02 17:21:29. That's five total adventures spent hacking there, not six. So it was only a level 5 site, not a level 6, which means that the lack of hidden files is as expected.
(account deleted) 26 Sep 2009 15:27