2. Encrypt files on the Dropbox server, in a "transparent" way, so that I do
  not need to use passwords to sync between org and Iphone (which I let Emacs
  do automatically once each day).

This is what MobileOrg's encryption is for. You set a password in your
.emacs and then the same one on MobileOrg and the files in
dropbox/webdav are encrypted, and there is no hassle.  Note that
MobileOrg only has encrypttion support in the beta 1.5, not the released
1.4 - I have a beta and am using it/testing it.