For what it's worth, olde school taxonomy relied a lot (mainly?) on morphological characters, characterized by the men (and women) looking at specimens in museums.  The trade used a number of approaches to deduce origins and reconstruct likely relationships.  Some morphological characters were deemed ancestral, others derived.  So there is a vast body of practice and knowledge that has produced fairly solid conclusions on whatever groupings and subdivisions one chooses to consider.  It clearly gets murkier and more arbitrary at the lower levels of classification, with subspecies/races/morphs getting into the realms of the questionable and arbitrary.  But overall, morphological separations are likely to carry with them differences in behavior, life history, physiology.  Specimens of honey bees in museums collected from populations prior to a lot of colony and queen movements may still hold some information on these ancestral relationships.  

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