As far as I know, you could do delta uploads with encrypted files. It should not be any different if the file itself is encrypted. For the same reason you can e.g. use rsync delta syncs with encrypted files...
I'm sure the rync delta transfer algorithm still works fine with encrypted files, but the changes for encrypted files are going to be calculated as 100% so you're not going to save anything.
You'd still need to pull it all down and apply the deltas each time you put it somewhere new, but it would work. Possibly with a 'full version' on some longer schedule. As a bonus, you'd get automatic history, which Dropbox stores anyway.
It's still got issues, no doubt, but it could be done, no?
There is also a project called ddar, which is designed to provide merely the de-duplication of tarsnap so you can setup your own repository (tarsnap only works with its service).
I don't think this is necessarily the case with all encryption mechanisms.