Mysteries of the Gunpowder Fort

There are absolutely no characteristic traces of the existence of a prison here, as a place of long-term detention of at least a number of people and their guards. And the location of the structure is not good to such use. Heating, water, household amenities and so on — how to organize it here? Although, there are many mysteries. For example, in the walls of the second floor there are such holes in all casemates strictly opposite each other. Why?