Why would they need it? They presumably aren't pretending that it's the
same character, just someone who happens to have the same name. Life
would become impossible for writers if they had to check whether every
name they used had ever been used before.
--
John Hall
"The power of accurate observation is commonly called cynicism
by those who have not got it."
George Bernard Shaw
An homage does not require permission. And Eric Kripke was a well
known fan of Doctor Who, he's also worked with Moffat.
Matt
Amy and Pond are relatively common names anyway. :-)
Imagine the nightmare if every movie / TV show had to ask permission to
use a name used in an earlier show / movie. Whoever first used "John
Smith" would be making billions, and we'd also be stuck with characters
with all sort of weirdo names from those creators who can't afford or be
bothered paying for the permission to use normal names.