The SiteShot extension uses wordpress.org mshot to create the thumbnails. These thumbs are created and cached by that service for 24–48 hours. If the site is down or at the time of creating the thumbnail, you’ll see the 404 thumbnail until the cache expires and the thumbnail is recreated. I have no control over the cached files and their expiration.
I browsed the first 5-6 pages of your directory and I think there are only 4 404/s and 2 “blanks” when visiting those sites half were (still?) down, so, everything does seem in order order… unless I am misunderstanding the issue.
I hope that helps!