When I read your post, more questions than answers come to mind! Starting with, "Who's your audience?"
My internet connection and computer aren't state of the art, but they're probably both faster than what the average user has. I doubt I'd have the patience to sit and wait for 200 thumbnails to load or - assuming the classifications are equal in size - even 50. I'd have to be mighty commited to seeing what you've posted.
The physical size of the images sounds OK to cover a range of monitor resolutions.
Is there a way you can break this project into smaller chunks to minimize the download time for given groups of pictures?
And, Save for Web will do a nice job of resizing the large images, but how are you going to create the thumbnails and then link them? Have you played with the Web Photo Gallery, which generates thumbnails and larger images that are already linked? You can choose your own size for both , and the images are customized for web viewing.
And I also think about 200 scans. Are these pictures small enough so you could scan them in groups and then let Elements do the resizing?