I see the problems of encrypting all content with a single key, so I voted for encrypting each document individually.
However, it would still be nice to encrypt everything with a single key during export (both manual and automatic). This would reduce the number of possible breaches from three or more (Dynalist server, Google or Dropbox server and every single computer or medium containing a manual backup copy) to just one (Dynalist server). And it wouldn’t induce the problems of end-to-end encryption.
(I know that there is a feature request regarding encrypted automatic daily backup, but I think that the above might be beneficial to your poll.)