I can't speak to Crusader Kings 2 specifically, but I have bought "complete" packs of games before, and any article you already have in your library will be sent to your inventory instead (so you can gift it to friends).
E.g. buying the complete XCOM pack activated all DLC in my library, but the base game was just added to my inventory since I already have it.
Steam seems to never allow you to activate something that already exists in your library, I've not encountered anything to contradict that so far.
Edit If you want to selectively split up the pack (not just what you already have in your library, but specific items) The single key translates to a pack on steam, which immediately activates everything (minus what you already have)
However, if you sent this pack to your inventory instead of your library, you can then choose which ones you activate.