Does an ATX power supply have any isolated outputs?
The outputs of the ATX power supply are isolated from the mains.  The outputs of the ATX power supply are not isolated from each-other.  In other words, +5V and +12V output "share" the same ground.

Multiple ground pins increase current carrying capacity.  I bet, you will see continuity between them if you check with a meter.

My information comes from several ATX power supply reference designs that can be found on the web (such as this one).  Such reference designs contain detailed schematics.  A complete schematic would be a bit too detailed for the purposes of this conversation.  But here's a block diagram.