The question is why they were destroyed. They are all homes to Princesses of Heart, so could Malecificent's plot have something to do with it?
I wouldn't be surprised, considering the time frame it could have been Maleficents doing or rather the unleashing of the heartless by Xehanort could have been the cause of the destruction of their respective homeworlds.
Another world that was destroyed was Pinocchio's home world. We know it was destroyed prior to Kingdom Hearts, so one could assume it would be in bbs, but it wasn't. Could Pinocchio's home world have been destroyed as a result of the Keyblade War?
Quite doubtful of that considering the keyblade war seems to be even before the time Master Xehanort or even Eraqus for that matter.
Several worlds such as the Land of Departure, Deep Space, and most importantly, Keyblade Graveyard just disappeared after the events of bbs. They weren't destroyed but they just disappeared and were never heard from since...even after Sora restored all worlds at the End of The World.
Land of Depature became Castle Oblivion so it didn't really disappear. As for the graveyard, it still exists, it just hasn't reappeared besides the Terra's sentiment boss fight because it isn't currently all that relevant to the plot of the series. That is until BBS, even then it was a graveyard; the remains of the war, aside from the war itself taking place there it really holds no more importance then the other disney worlds like the Pride Lands or Olympus Coliseum.
Also, it's not just at a story standpoint, it's also to keep things fresh for the player. Worlds that had a completed plot were left behind, while lands that had more backstory that could be added were included in further KH sequels. What I mean by this is movie tie in's since then could be written into the plot of the game or rather plots from the original movies being tied into the plot.
Btw, Deep Space wasn't a "world" in the conventional sense, just a level that took place in a certain area of space.
Could Vanitas have caused an imbalance just as Xehanort predicted? And could this imbalance have fragmented the structure of the universe?
Considering Vanitas' demise has wiped away the existence of the unversed, the main threat at the time, his influence on the KH universe is small compared to his masters future incarnations deeds IE creating the artificial heartless, bringing the heartless out of the dark realm to attack the realm of light etc.