Art director JJB said:

“Sadly, you are not missing anything. The only purposeful and thematic intentions in relation to the hexagons are in the Hive Club in Lower Hengsha. Because it is called the Hive, I thought it made sense when the concept artist proposed the honeycomb visual direction for the location. Also, because it is Tong’s hangout spot as well as some of his men, I thought the analogy with a bee hive made sense. This bee hive idea was even then included in some dialogues and extra story bits.

See, in reality, I truly dislike hexagons as an aesthetic choice. I think they are way too overused in futuristic video game designs. Now, this being said, it is true that they are still a certain amount of hexagons in Deus Ex: Human Revolution. But whenever they are present, it is either because I thought they made absolute thematic and contextual sense, or because I overlooked them when they were created (it such a vast game visually speaking that sometimes I just couldn’t review or see everything), or because I got lazy and just said what the hell (It happens… LOL).

To summarize, you are absolutely right about the black and gold being an informed analogy to the Renaissance. Also, the black represents the dystopian cyberpunk side of the game, and the gold represents the humanistic side. And as far as geometrical shapes are concerned, the true iconic shape of Deus Ex: Human Revolution is the triangle. It is thoroughly and deliberately layered all over the game, and it does have a true underlying meaning in relation to the game’s motifs and tropes.”