We have some default limits explained here: https://itch.io/docs/creators/html5#zip-file-requirements
The rational is also explained on that page:
Why do we have limits? Although many game engines allow you to export anything as an HTML5 project, often you need to consider what the user experience of playing the game will be like. You can think of an HTML5 project like a website: many of the same performance optimization recommendations still apply. We have these default limits to encourage developers to consider how their games are distributed
But, we’ve had a more engines these days hitting the old 500 file limit, so I’ve bumped it up to 1,000 files.
Note I did a quick test on your page to see if it would load and it failed, but it looks like it’s because of how you packaged the page. There is an index.json file but it’s not where the engine is looking. Hope that helps you figure it out