I think people are mistaking things 'disappearing' due to mechanical reasons with things 'disappearing' for lore reasons.
The bodies DON'T disappear, we just don't deal with them, usually.

For one of the main storyline quests, we schlep several bodies to a cart for disposal and burial.
For at least one of the Hildibrand quests, we follow a trail of corpses.
For that alchemist quest, that body was laying around for over five years, probably preserved since it was no worse for the wear. It 'dissolved' more or less for thematic reasons, possibly because it returned to the dust it should have been when it ran out of magical mischief to hold it together.

In short, the bodies hit the floor, the spirits within hit the door. Their 'spirit' would return to the aether, if nothing else. The body just gets buried or fed to the Ul'Dah refugees.