It could be an inspection hatch. Page 51, in Warship Pictoral 15, Kriegsmarine Schnellboote, shows schnellbootes during construction. There is a pic of a standard bridge S-boat with a partially completed raised foredeck which shows the gearboxes and shafts for raising and lowering the torpedo tube covers. These appear to be in the same approximate location as the the objects in question on the later armored bridge boats. The "hatches'" would likely be required for servicing the gearboxes and shafts.
Jim