Nuka Cola Caps are as good a currency as anything else since there is a finite amount of them. They are not being produced any more and are hard to counterfeit. The metal is probably the cheapest they produced at the time and is not good for much of anything else.
I do accept the reasoning behind your thinking but have to throw my hat in with Styles on this one I'm afraid.
Think of caps more as a credit note from water merchants, it is impossible to carry that many days worth of water around on your back, so much like say modern store gift vouchers,you redeem them as and when you require for convenience, but only participating outlets will accept them. Therefore giving them value. They are not the de facto currency.
There is a finite amount of them but they are not that hard to counterfeit, NV has a quest where you are employed to smash a press to stop fakes being made. Just being rare doesn't mean something will have value, in the anarchy of the DC wasteland, survival is the only concern for most people, weapons, ammo, shelter, clothes, water and food are the only things with any actual value.
Without a government to back it, no alternative currency would ever be instigated and couldn't survive any lack of confidence in it ( just look at the Euro, no single government but a single currency? Was always bound for failure ) so, as there is no governing faction in FO3 a system of bartering would be logical.
I'm not saying caps CAN'T be used as a currency in theory, just in FO3 they shouldn't be because there is no story to explain how starving, frightened, cold people separated by large distances and scary beasties, all suddenly one day spontaneously decided to swap that perfectly good combat shotgun, ammo and what little food they had for a bag of pre-war bottle stoppers?