If beast races are treated as subordinate by the dunmer, why are many of them high members of society? (ie shopkeepers, guild masters etc..)

If you're reffering specifically to Morrowind (the game) then you must keep in mind the influence of the Empire. While the beast races are often kept as slaves, Imperial law makes sure that people who are not slaves have full rights as citizens. This, however, does not protect them from less overt discrimination within Dunmer society. It is worth noting that most high-ranking Khajiit, Argonians, and Orcs (not actually a beast race, but considered to be so by many) are within Imperial organizations, such as the Mages Guild and Fighters Guild, as well as the Imperial Legion, and most beastman shopkeepers are within Imperial settlements, or the Vivec Foreign Quarter.