How does QCS handle objects that are hidden from publisher's GAL?
The behavior is by design.
Objects hidden from the GAL are not synced.
1. If object falls under the publication's scope but was originally hidden from the GAL - no QCS stub object will be ever created in the subscriber's environment.
2. If object was initially published but later on gets hidden from the GAL - QCS removes all exchange attributes from the stub object thus making it excluded from the subscriber's GAL. However AD object is still present during retention timeframe. Please also see the following Quest KB SOL31272 as retention mechanism behind synchronization of deleted and hidden objects is the same:
"How does the synchronization of deleted objects in QCS work? Is there a retention period?"