What happens if 2 references of a named NPC are placed in the game world, and in different locations? For example, let's say I "accidentally" placed an extra copy of Thoronir - a Market District character - inside Vilverin. Would the extra copy actually eventually find its way into the Copious Coinpurse and start behaving exactly like the original instance? Would the game mess up really bad?

Does Oblivion actually have any built-in mechanics that deal with duplicate references of the same NPC?

Both references have the same AI packages which are defined in the base, so both are going to try doing the same stuff at the same hours. So yes, in theory your copy will try to get to the Copious Coinpurse and offer services. Reference ownership in cells is defined to be a base faction or NPC so he will likely sell the same stuff than the original.

But the new copy will have a different RefID, so any script referencing the original Thoronir will not, or at least probably will not, affect the new one. Nor will any condition in dialog and such referencing the original Thoronir reference, instead of the base Thoronir object, apply to the new one. Also, the new copy will not have a merchant container from which to sell stuff, which you need to define on each reference (if at all).