Is there any reference management software that supports hierarchical tagging?
JabRef is a reference manager using the BibTeX format. It uses the concept of groups, i.e. papers can be put into groups, and it allows to create a hierarchical group structure. Since one paper can be put into any number of groups, it is essentially hierarchical tagging.

With JabRef, one can even configure for individual groups whether a group will automatically include the content of any subgroups (analog to tagging), or will include the content of any supergroup (refining), or just include the papers assigned exactly to this group (as in a classical folder structure).