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I am creating a zip archive containing two identical files at different paths. Does the zip archive format support something akin to the Unix concept of hard links? By this I mean the ability to store the file only once (saving space), but to index that data blob to two different paths within the zip archive.
If the file format does support this, how could I go about creating such an archive using free tools in Ubuntu?
No, the Zip file format does not support this. This is because the Local File Header contains information about the file, including its name, followed immediately by the compressed data for the file. It is not possible for two different Local File Headers to point to the same compressed data.