I was just reading Why Hexagons pt. 1 and I recalled how I puzzled over the structure of the Library when I first read the short story a few years ago as well. What I came up with was something like this:

The text is taken from here and there are some slight differences in translation e.g. “hallway” instead of “vestibule”.
At first I thought I might be taking some liberties with the description but actually I think it fits the text better than the versions you show, with the key being the positioning of the air shafts and the word “between”. The text says “hexagonal galleries, with vast air shafts between, surrounded by very low railings”. My version does in fact show air shafts between the galleries, whereas yours shows them in the middle of each of the galleries. In mine then, the mysterious second free side is simply open to the air shaft! It would also have to be possible to walk around the air shaft between galleries (otherwise you would be stuck to a group of six galleries just as if there were no hallways/vestibules) but I don’t think this contradicts anything in the text.
What do you think?