There are numerous trap doors in the topside deck of a fleet boat's superstructure. They provide access to compartments that store things such as mooring lines, torpedo loading cranes, as well as access to the main vents, air induction lines, mufflers (yes, fleet boats had them), air flasks, bow plane rigging gear, the tops of the ballast tanks and scuppers for chipping, cleaning and painting. Life rafts, and in the early Gatos, motor boats were stored below decks as well. The main induction valve(s) are located below each boat's "cigarette deck."
I have to question if something as precise as spare armatures were stored in the superstructure. First, the U.S. Navy learned before the war that that was a very rough place to keep sensitive things and that's why it designed its boats with storage for torpedoes inside the pressure hull, starting with the Tambor/Gar class; no more "external" storage for torpedoes and attempts to install external torpedo tubes were failures because the "fish" took a beating and could not be properly maintained.
Second, a spare armature for a main propulsion is huge and heavy, and there would have been no way to get it from topside storage down into the motor room at sea without removing at least part, if not all, of the control cubicle. I believe any main propulsion armature needing repair would have been done so in place by the resourceful electrician's mates or at a shipyard. Remember, most of the fleet boats built during the war had the four-motor propulsion configuration. Only later in the war did they devise a two-motor setup with a large motor on each propeller shaft. A spare armature for a motor-generator set could have been stored somewhere in the pressure hull.
