That is true – here’s one way to speed this up. After your first export, you’ll see if you click on the Dropbox icon where those files are going. Hype uses Dropbox > Apps > Hype > Export > DocumentName as the folder structure.
If you move those files into Dropbox > Public (on your computer – not in the web interface), you can ctrl + click on the .html file to get the public URL of your document. Then, when you export to that folder for subsequent changes, only the modifications will be reuploaded. This requires that for your next export (or even your first export) that you export as File > Export as HTML5 > Folder – and select your Dropbox Public folder.
We are working under the constraints of the Dropbox API unfortunately.