That was about whatsapp doing a major goof and putting private files in a "public" area (every app already had a private area for file storage) and failing to secure them properly (encryption is hard, apparently).
Removable storage, SD, USB, etc, was moved from external_storage to media_storage with Android 3.1.
Note that external_storage was still about putting files in an area readable by any and all apps that had read_external_storage permission.
In other words, the change would do jack all to safeguard against idiots like the whatsapp app devs.
Sure there was! Simply generate a random key, store it in the (small) private storage area, and use it to encrypt whatever you want to write. Instant private area!