Are you sure about the main store? the bomb went through the after engine room (I remember looking into the hole from the starboard side). Some changes were made to the layout in the area of the stores some years later to accomodate female ratings.
She was brought back to Pompey for repair. An oppo of mine was at HMS Sultan with me and was drafted to FMB to repair her. He said the engine room was a mess. Apparently the bomb went through one side hit everything and left through the other without exploding. someone up there was looking after the boys that day.