When you add a file to Hype, a link is made to that file and it is also copied into the filename.hype file. When updating that external file, you're asked in Hype if you want to update it. As much as possible, the actual .hype file is trying to be the container for all media, images, etc. You could dig into the actual Hype file and find the resources folder to make modifications to files, but keep these things in mind:
- If you modify any image dimensions, Hype won't know about this change.
- Hype will optimize images during export, so any compression you do on images in this folder may not carry through unless you uncheck 'Automatically optimize will exporting'. Check out this section of the docs for info on how images are handled: Image Optimization
This is a good suggestion. Is your main pain point the after-export compression step?
If you're just working in Hype and adding assets to your document it shouldn't create any folders for you. (Though there is a bug where on some network drives a folder is created temporarily during saving -- this is sometimes not deleted).