Think of two layers, one on top of the other. The lower layer was there first and carries the weight; the upper layer was added later and depends on it. Super- means above and structure means a built thing, so superstructure is simply the layer on top. On a ship it is the cabins above the deck, in a building it is everything above the foundation, and in writing about society it is the laws and ideas standing on the economy. The word is about position, not about size or importance.
From the word’s history
Wiktionary gives super- + structure, with super- from Latin super, meaning above. The literal reading - the thing built on top - is still exactly what the word does in both uses.
字典把這個字拆成 super- ＋ structure，而 super- 來自拉丁文 super（在…之上）。字面就是「蓋在上面的結構」，今天的兩個用法都還照著這個字面走，一個蓋在船和樓上，一個蓋在經濟上。
Wiktionary, "superstructure"
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