Possible use cases for an empty span that I can think of off the top of my hat:

• Clearfix
• As a placeholder that will be filled/replaced by javascript
• As a placeholder that will be filled/replaced by a pandoc filter
  
• As an anchor for before/after pseudoelements
  
• As a container for a background-image
• As a piece in some CSS trickery to get fancy effects without images
  
• To have the right count of elements for some table-like presentation
  
• Because of symmetry with some other structure where there is content inside the span

There's probably a lot more, these are just some cases I thought of. Is an empty span always the best solution to these problems? Probably not. But sometimes it is.

The most relevant as it relates to pandoc is probably the third one: in a pandoc filter. Because of that I would not want to see this feature be removed.

Now, should the span be self-closing? That's a different question. I suspect that that's the main reason for many/all of the errors you're seeing, not the pure empty-ness. So that might be something worth changing. But as you're saying, that's a Hakyll problem, not a Pandoc problem.

Cheers.