On Debian Wheezy with KDE.
I have a file /etc/apt/apt.conf.d/20noperiodic.
And I can confirm with apt-config dump, that these are set and that apt-get won't automatically update.
In Apper settings fetching updates is still set to hourly by default and I believe it is a bug and APT::Periodic::Update-Package-Lists "0"; should be honored.
PackageKit doesn't read that file, as it's an abstraction layer above apt/yum/etc.