So if I have a VCX with Ghost title and FCS, no other upgrades, and I have the shuttle docked, and the shuttle has an auto blaster turret, how does this work?

Does FCS activate when using the turret on the shuttle whole docked?

Can you even do a second turret attack from a docked shuttle if the turret is not on the VCX?

The docked shuttle and its turret effectively don't exist while it's docked. You need to have the turret be equipped to the VCX in order to be able to attack with it, both normally and for the special title-enabled attack. If the VCX only has FCS and Ghost equipped, but no other upgrades, it can't make any turret attacks at all. If it does have a turret equipped, then FCS and the turret interact and work as normal.