True ... but they are still names in use, names being given (for whatever reason) and names which have their own fashions ... it seems churlish to ignore them! Does this apply to all the popularity charts on this site, do you know, or do different countries do things differently?
Wouldn't two lists be the real answer? One for the first names only, and one for all given names lumped together? It would be simple then to see how the distribution worked.
As for middle names ... my cousin Robin Thompson has Arthur as his first name, though there was never any intention that he would use Arthur. Wouldn't you rather be ART than RAT? My husband was given Ernest as his first name, after his father, who was named after a friend of his father. Neither of them ever used it, and our son is glad to have escaped ... .
Also, I suspect that middle name fashions change in the same kinds of ways as first name fashions, only more slowly. It would be nice to know for sure!