At the end of the story, why do all of Tom's possessions disappear or get destroyed?

This is a great question! The narrator doesn't tell us why, but we could take some good guesses based on information from the story.

First, let's take a close look at that spot:

"Trustees were appointed to take charge of Tom's effects. There was nothing, however, to administer upon. On searching his coffers all his bonds and mortgages were found reduced to cinders. In place of gold and silver his iron chest was filled with chips and shavings; two skeletons lay in his stable instead of his half starved horses, and the very next day his great house took fire and was burnt to the ground."

So after Tom was carried away by the devil into the swamp, which was set on fire, all of Tom's stuff, too, is found mysteriously destroyed: his financial documents have been burned, his money is turned into little shavings, his horses are not just dead but skeletonized, and his house burned down.

Why? Again, it's a matter of interpretation, but here are some ideas.

1. Tom only got all that stuff through his horrible business practices and the treasure he got from the devil. So, it wasn't just Tom himself, but also his stuff that was "dirty" or "rotten" in a sense. It wouldn't make sense for such horribly ill-gotten goods to be used by the more morally upright members of the community.

2. Just as the devil had control of Tom, so too did he have control over Tom's things, like his money, his horses, and his house. And we saw that the devil likes to operate in style here. He didn't just stab Tom and then leave, for instance, when it was time to take his soul; instead, he swept Tom up onto a black horse and whisked him into a swamp during a lightning storm, then brought down a lightning bolt to set the swamp on fire. That is showmanship. He would probably burn up Tom's things to really cap off the whole deal.

3. The destruction of Tom's things gives the narrator something else to talk about during the closing paragraphs of the story. After readers see that whole dramatic capture that ends in Tom's death, the ending of the story might be kind of awkward or sudden if we just got the description of how the townspeople kind of stood around confused and then got back to business as usual. "Well, that... happened," the narrator would seem to say. The images of the skeletonized horses and the burning house are entertaining, and they help round out the story.