index.html - can I take it out from CI in a safe way?

A index.html file outside the document root is indeed useless.

I would not just delete all of them because perhaps in the future you want to switch to a different hosting company who does not allow you to upload files outside the document root. You will need to include the application folder and systems folder again into the publicly accessible space.

If you switch to a Windows host (iss) your .htaccess would not be read. Thats why I don't believe its a good advice to delete all index.html files and rely on .htaccess to disable those index pages.

The index.html files don't really take up any serious space, they don't really stand in your way and therefor I see no reason to remove them. Besides, you will have to remove them every time again when you download a update of CI...

It's not about space... It is just one more thing to worry about. If having application and system outside of public_html is a standard (even if it's only a personal standard) I can at least not worry about having to create index.html for each module.

About the update I don't really touch system folder anyways so I will leave it as it is and can even copy paste an update to it if needed. As to application I can't update without checking the changelog