I think it became a wasteland when all cutie marks were erased since you’re effectively removing everyponies personalities, aspirations, and motivations to be unique. If the show wanted to be real morbid, I think the chances of no pony surviving are high due to no real reason to. Well. Live. Living without any aspirations, talents, personality, free will or thought is just a life living in a shell of yourself. At that point, it would be easy to assume everypony just went extinct, not wanting to continue that suffering.
On the other hand, if any pony survived it would be likely that they are simply living a sad quiet life. The reason it may appear so barren would be because they live elsewhere.
Twilight could have also been making a point to Starlight, while I don’t believe she would lie purposefully this may not have actually been the future.
In this timeline, the elements of harmony were probably lost to time :p
With nopony able to hold the position or use the elements, they have no purpose.