@Background Pony #80EF
 

It’s a common Misunderstanding. Applejack’s parents aren’t dead.  
Well, not any more.  
They WERE dead, but Pinkie Pie went and gathered all the Dragon Balls.  
Now Vegeta Apple and Bulma Apple are off travelling the universe in spaceships, as seen by in the night sky during the Apple Family Reunion, going off to Namek to stop Freiza.  
Applejack wants to make the reunion the best reunion ever to celebrate her parents’ return to life, although she is upset that they continue to do something that killed them.

@the-pieman  
Apple Family Reunion episode, when Applejack is vowing to make it the best damn reunion ever.

@The Chaos Hunger  

@the-pieman  
Faust confirms it, as far as I know. It was intended to be the implication at least, what with the two shooting stars, never mentioning nor seeing them and the hat.

@the-pieman  
It’s been pretty much confirmed by the show staff at this point, though not explicitly stated in the show.
 
The two shooting stars in the Apple Family Reunion were representing Applejack’s parents, according to the storyboarder.

prove they’re dead. Just because we haven’t seen them doesn’t mean they’re dead. How about you? I’ve never met YOUR parents. GASP! I’ve never seen them, so they must be dead!

“Like I said. Everyone is happy. And my parents are dead. They’re not mutually exclusive.”

Well not everypony isn’t an advanced magical unicorn/being. It is probably would of been rare to have one nearby her parents. This is assuming magic dealing with immortality is legal

 
“At least you have a brother and sister…”

Yep…this meme still exists…

And where ancient chaos Spirits, Zombie kings, shapeshifting bugs, and moon death horses attack daily

Meanwhile, Fluttershy and Scootaloo have a big old question mark on “Family”.