Configure the profile to backup to zip files and then set the Level of compression to zero from the Compression settings page. Next, set the encryption method and password as appropriate from Modify profile > Expert > Compression settings page (for V9 and older versions, go to the Compression > Encryption page to set the encryption method and password). The files are still stored in zip files (encrypted) but no attempt to compress them is made.

With SyncBackPro/SE you can also encrypt the filenames inside the Zip file.