Everything is a hierarchy, even the tags in your mind do belong under some tree/node like imagination. Tag is essentially just what you described "duplicates or symlinks or whatever."
This isn't really true. Even mature, sophisticated attempts at making hierarchical classification systems (e.g. the UDC[0]) don't claim to have created a system where each document gets a unique leaf on a tree, and indeed instead attempt provide some syntax for adding additional metadata into its "nodes," i.e. the nodes become the sum of their tags.
[0] https://en.wikipedia.org/wiki/Universal_Decimal_Classificati...