There is NO WAY at all for the e-reader to store THAT much data. I mean c'mon, its used to read literally thousands of different cards. And the e-reader is so small. How exactly do u expect it to store the info of so many cards? Not to mention FUTURE cards as well. Even if it could store that much data, i dont think Nintendo is so kind as to sell it at such a low price.
Its more than possible to store data in those dots. How do u think ATM cards work? Its more or less the same principle. In any case, the total memory of those 'dots' is no more than a few bytes anyway, at most 5kb, tho i doubt its that much.
So yeah, theres ur answer. But u know, i believe some sites (dunno bout the official one) already has articles from Nintendo on how the dot-matrix work.