in this case S6 doesn't start/manage this daemon, s6 only start what you ask to start (we are not on system:D here). This daemon is started by some applications (certainly browser as said fungalnet) passing through Dbus. Same things for gconfd-2, ati-spi-* and so on.
S6 only manage what you ask to manage and never take decision to start, enable a service by itself or passing trough Dbus. Take a look at /usr/share/dbus-1/services, you should fine into this directory something called org.zeitgeist (something similar). If you rename or move this file, you will see that the daemon do not start anymore.
A daemon managed by s6 have a s6-supervise program which control and manage this daemon, under htop something like this :
|_ s6-supervise cgmanager
|_ /usr/bin/cgmanager
if you do not see s6-supervise program above that significate that the daemon is not managed by s6* program.