One benefit of this would be reducing the need for broad, "field-specific" tags. Electronic-structure programs like gaussian, qchem, molpro, etc could all be classified under electronic-structure or quantum-chemistry. Molecular dynamics programs like lammps or gromacs could be grouped under molecular-dynamics.
It would let questions have as specific of tags as possible, while still making them searchable under the most general terms. We currently generally discourage tags with only a few uses, but this wouldn't need to be the case with hierarchical tagging. For example, you could have a tag for any of the many multiconfigurational or quantum monte carlo methods and classify them all under a general parent tag.