Hype's data for animations and page structure is stored in a JSON format and the export is not meant to be editable. The hidden divs you are seeing are probably those meant for SEO support (so text content still gets read).
If you want to attach specific styles to elements created in Hype, you can go to the Identity Inspector and add a Unique Element ID or Class Name. This can then be referenced in any of your CSS, including that created by going to Edit Head HTML in the Document Inspector. You may need !important directives if the styles are overriding that which Hype would set, or unchecking Protect from external styles if you are targeting the Inner HTML of Hype-created elements.