I use a form of economic warfare when attacking enemies, in that I try to target their most wealthy cities first in order to cut of their cash flow and thus their supply of reinforcements. I find this works very well against the HRE, taking vienna essentially stops them building any decent sized armies.
Though it's an interesting idea to use assassins to destroy their economic buildings, I've tried this in the form of "psychological warfare" before to make cities rebel, but I guess it could work very well to knock out an important port or mine on the eve of war.
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