Cocoa Beans do not spawn in dungeon chests.

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.