First I made an issue at WorldEdit issue tracker, but they told me it's a bug in Spigot so I report it here. Link to WorldEdit issue: https://github.com/EngineHub/WorldEdit/issues/1924

So the issue is, if you use the WorldEdit /superpickaxe single, it destroys items like in creative and drops them. But if you try to break a chest, it drops the chest and deletes the items in.

The developers said, they call the API to breakNaturally, but spigot doesn't drop chest items here.