A lot of my thoughts & explanations on eons are over here, where I wrote about the “Goblet of Eonothem.” tl;dr an eonothem refers to the huge layer of rock that covers the earth during a period of time, while an eon refers to the period of time itself.
Eons pretty clearly represent the passage of time, so it makes sense that it would be used as the title for pieces like hourglasses, watches, and other timepieces. Many of these pieces have stories about people running out of time, a theme we encounter a lot throughout the game.