Three identifiers, three different layers
A Salesforce Commerce connection asks for three identifiers, each pointing at a different layer. The short code is an eight-character routing code that sits at the front of the API address. The organisation ID says which organisation to connect to, and the site ID which site's data within it to read.
The third matters most on multi-site installations: each site can have its own product catalogue, prices and currency. A connection with the wrong site ID works technically but works against the wrong catalogue — it raises no error, it simply does not bring the data you expected.