Is it ever implied anywhere exactly what happened to Doc Hudson between the events of Cars and Cars 2? At I've point one of the characters says something like "doc would've been proud of you". I assume the reason for the character's exclusion is because Paul Newman didn't get signed up.
Paul Newman died in September 2008 and, although the pre-production on Cars 2 was already in full swing, he was either too ill or already passed on before it came time to do the voice acting.
The scene you mention in your question is a touching homage to the legend that was Newman.