The default file count limit is to encourage people from uploading projects that aren’t optimized for play in the browser. If you have thousands of files then I strongly recommend making a downloadable version of your game. https://itch.io/docs/creators/html5#common-pitfalls
From the common pitfalls section in the link above:
Uploading a very large game — 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. For larger games, it’s often better to go for a downloadable version. This is why we have default limitations for project sizes (although you can contact us if you need lifted limits). Projects can still be easy to play with the itch.io app. You can think of an HTML5 project like a website: many of the same performance optimization recommendations still apply.