Same happen for Crusader Kings 2.
They try to reduce number of DLC by merge some of the old. For example, Crusader Kings II: Ultimate Portrait Pack is a new DLC with 11. The bundle have 43 items and there is only 18 DLC for EUIV.
And now the bunble give wrong information. They say -15% compare to individual price for CKII , but it is not true. The price of bundle is almost the same than DLC inside + game.
If I buy the bundle, I will over paid because I already have some of the items (for example : I can buy Digital Extreme Edition Upgrade Pack, but I already have The Stars and Crescent, The Horsemen of the Crescent Unit Pack and The Conquest of Constantinople Music Pack).
If I buy the DLC in the shop, i will overpaid because I already have most of the item of the news packs.
I dont really understand paradox ... They could propose to the players to check all DLC they have and give a discount for update to new pack depending on how DLC we have. But no, they dont ... They just take the easier and lame solution.