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What's the best and quickest way to deal with either of the two?

in the dutch case, if you own any or just ONE of their provinces, release it as vassal, thus the ai events will trgger and the 1 prov vassals becomes 4 at least (or more depending on mode):D
the dutch revolts are one of those special circumstances were you can increase you domain 10 years later with no sweat ( a bit longer if catholic nation since u have to wait for edict of tolerance to dilo them again):)

the hugenots; better release them before the war of religions thus getting bb decreased ( if event forces you to cede them provinces you do NOT loose bb with those "forced" commands). and the slowlly get them back when possible. again an excelent way for france to loose bb in this case, if has had accumulated a lot previouslly;)
 
Actually I just played through it again. Giving them everything they wanted pretty much kept them from ever rebelling, though it did cost me a ton of Centralization.

As for vassalizing then annexing later, that feels like it'd be a little bit too gamey.