Well I can start by saying that there is some sort of Lore Reason and there is not (Please take this with a grain of salt. Not everything in Dark Souls games is related to the Lore).
But I will say that believing there is an actual Lore Reason depends on you and how much you read into the game's Lore. For my honest belief read the Not so Lore Reason part of the question
1. Lore Reason
In Dark Souls there wasn't many vanishing corpses of enemies. But there were some. The Lore reason for this is that some of them (enemies or not) were conjured illusions. They were not there physically per say but they were there as an illusion. So basically when you killed them they would simply vanish.
2. Not so Lore Reason
Some enemys have a vanishing effect such as demons.. other enemies stay there until you move far enough away/stop looking at them. It doesn't matter because in the end all enemies need to be culled for performance reasons.
The only reason Dark Souls 1 didn't do that was literally because it was a bad/lazy design choice. In the world of game development, the idea of leaving corpses everywhere is considered bad design because they serve almost no purpose and cause a massive dent in performance and loss of memory.
So, regarding performance and smoothness, small enemies with small bodies would not be so bad to keep the bodies around for a little bit. But really big enemies might slow down the game a bit. So, by design, they make them vanish to keep the game flowing well.
Why not add some small placeholders for these enemies? (comment by @NamikazeSheena)
Well that is a good question but it all comes down to Game Design and compromises for performance sake.
Let us compare enemies in Dark Souls 3 for example (the most recent entry)
- Lothric Knight: Not that big. Semi-Complex textures. The engine handles them well. So basically their bodies can be left for a little while (if you remain within their draw range)
- Fire-Breathing Dragon: Huge. Big Textures. Already slows frames per second down when on-screen. Performance wise it is NOT viable to have all these bodies just around.
When you distance yourself quite a bit from the bodies. Some memory can be released to draw the new areas and present new stuff. Thus, old stuff must go.
People tend to overthink Dark Souls lore in general and read to deep into it. In this case right here most of it is just plain performance and game design compromises.