Personally - no, there is no reason I would use three.js layers in their current incarnation. I can imagine some might use them to hide things temporarily, it can be “convenient” perhaps.
In meep, I use a concept of layers, but it is more akin to using separate groups at the top level of a scene and there’s a full-brown visibility set solution on top of that, so it’s a fundamentally different implementation approach.
I use that version of layers to aggregate various renderable categories, such as trails, particles, terrain and foliage. Using layers this way, I am able to partition the scene in such a way that a system responsible for particle rendering can safely work with it’s renderable objects within the scene while being completely unaware of the rest of the renderable objects. It’s information hiding for the most part.
Another aspect is visibility culling, different renderable objects categories can have different visibility filters.