I have seen info about how the stones' price will change with your style, but I haven't found anywhere if each can be bought more than once.
After receiving all the Mega Stones from the vendor, he will not offer any more. However, I have not yet tested whether he will sell them again if you lose a Stone (e.g. through trading). So, until I can do that sort of testing, I have to say that you cannot purchase the Mega Stones multiple times.