- Everybody got it.
- Everybody who didn't get it is keeping their mouth shut.
- Nobody cares.
So you see, "gone" in beatnik slang means "really good" as in, "that Charlie Parker is one gone cat".* It's just like the way you or I would say "awesome", "rad", or "badass". Crazy, huh? But those were crazy times. Of course they were all so "hopped up" on "tea", "goofballs", and "bennies" that they barely knew what they were saying anyway.
Now, back to our joke. When the beatnik asks for some apple pie and the waitress says the apple pie is "gone", the beatnik thinks she's saying the apple pie is "really good", and hilarity ensues. Ha, ha! "Dig"?
Wait. Where's everybody going? I've got lots of other jokes I can explain. Come on, guys. Things were just getting fun.
* Of course, the beatnik is not actually calling Charlie Parker a cat. "Cat" is beatnik slang for "cool guy".