"A given hash uniquely represents a file, or any arbitrary collection of data. At least in theory."
No. No. No
A given hash does not uniquely represent a file, or any arbitrary collection of data in theory, but if well designed it can in practice.
You actually understand this (because the rest of your article explains just why there are problems if the hash function is no longer deemed secure) but utterly misstate the problem in your first line!
The whole point of reasonable output sized crypto secure hashes for identity is that the probabilities of collision outweigh the fact that collisions are, in the infinite sense, inevitable.

Hashes are a bit like fingerprints for data. A given hash uniquely represents a file, or any arbitrary collection of data. At least in theory. This is a 128-bit MD5 hash you're looking at above, so it can represent at most 2128 unique items, or 340 trillion trillion trillion. In reality the...