That is the case for at least some of the articles. There are also quite a few initialized projects but with nothing inside of them. And the overall file count comes from things like saved email templates that they have sent out, etc. Node modules, and a lot of other garbage files from Terraform, Ansible, etc.
On some special days, the crossword puzzles even generate a clever, witty animation that goes along with the hidden theme. In other words, an easter egg.
They're different enough so I could see that they create a separate repository for each special version of the puzzle.
It sounds like they host all their dependencies and just cloned a lot of them to have them under control.
I can’t see the newspaper writing enough code to fill 5000 repositories.
There is a chance they use repositories for data or archives. Then it could make sense I guess.