Well, you said it all in your post. There must have been thousands--hundreds of thousands--of feet of film that was never used; and yes, it is probably lost or has been destroyed. I bet everyone on this board would love to see every inch of it.

Here's a detail about one of the deleted scenes included on the "extras" disc of the DVD boxed set:

When Michael is giving his blessing to Francesa and Gardner Shaw's marriage, the scene ends with Michael telling Tom: "Make sure her dowry is big--these people think Italian brides go barefoot." But, the "Saga" version seen often on cable has about 8 seconds after that: Michael turns to a hulking young man in a plaid sport coat and says, "How's the football, Santino? He replies, "Fine, Uncle Michael." That's Sonny's (probably oldest) son. Frank (who gave Vito the get-well card when he returned from the hospital) is probably Santino's younger brother.