In Beta 1.4, Cocoa Beans were made to spawn in dungeon chests, the only way to obtain them in survival mode before 12w19a. Cocoa Beans remained as a reward in dungeon chests up until 13w36a, when jungles became rarer. Whether the removal of them in dungeon chests is a bug or intentional is beyond my knowledge.
Invalid
Yes, they were removed. Asking for adding them back would be a feature request, and... well, this is a bug tracker.