As I see it, the mission CB's represent CB's that were acquired by special means (for example: your nobility took care to create a reason to invade that province, "Save our Brethren in provicne x" CB's make sense in itself, subjugation can be considered as returning some minor nobles from other countries their old rights, etc.) and how they were exactly acquired is left to player's imagination.
Still, all that looks rather fishy. I'd agree with Nicolas19 that mission-triggered CBs are over the top. You take a religious mission as an example, but that's actually more of an exception. Not all of the conquest or subjugation missions have any legitimate historical reasons behind them. Far from it. I'd say most of them haven't. It's just plain old greediness and power-thirst.
Say, when Muscovy has missions to annex nearly all Russian states, when France absorbs minor French states, when China eats up its neighbours, when England conquers Scotland, Ireland and France (!!!) - what is legitimate about it? If it's about uniting the nation - you have a separate CB for that. If it's about claims to the throne - that's also covered. Why have an extra CB to make it easier?
In history, you had to find legitimate PRETEXTS, sure - to keep it decent (that is, in EU terms, to have a CB). And I believe that it should be left to the player to find a pretext. That would make you think. You have nationalism, religions, SoIs whatever. Maybe, throw in a few more espionage missions to sway the public opinion. In some cases you should be forced to attack with no CB. Who said completing missions must be easy? Getting a CB just as a free hand-out looks like a spoiler.
Moreover, this gives major powers another unfair advantage (I was always irritated at this 'lucky' thing - fortunately, it can be turned off easily, unlike this powergamer-friendly new CB), and pushes them to play in a 'historically correct manner'. Everyone who has conquest or subjugate missions is now more powerful. If we return to Muscovy, they now have better odds against their neighbours. Moscow has a way to legitimately attack them, but they don't. I can't see any logic in that. If it's because Muscovy did conquer them in real life - well, that's just stupid. I don't know about the others, but I play historical games to REWRITE history, rather than repeat it. I believe that at least should be an option.