Probably not.
If One Piece does end up getting some sort of sequel, like Boruto or Dragon Ball Super, chances are they'll want to keep one of the main power systems of the world intact.
If anything, I kind of expect a brand new crop of Devil Fruits to be born or to be grown all around the world. Teasing a whole new generation of Devil Fruit users and their crazy powers all inspired by the events of the main manga.
I think the Devil Fruits would only cease to exist if we replaced it with something effectively the same. Like maybe everyone gets access to whatever is giving the Gorosei their powers, maybe? Maybe that turns out to be a "purer" form of the Devil Fruit's power? But, otherwise, I think Devil Fruits are going to stick around.
I understand the logic behind kind of expecting the Devil Fruits to disappear, though. As a metaphor for childhood's end and all that. Or letting the ghosts of the past rest. But, I just don't expect that to end up being the case. Sometimes you need to be a little childish.