Kind of. If you destroy Lübeck then some of the north German provinces might start trading through Stockholm - but others will switch to Antwerpen or Venice or wherever, since they'll be closer or on better terms than they are with you. So you'll get a proportion of the CoT's current income, but not all of it.tl;dr - Will destroying one center of trade raise a nearby center's value?.
You'll also get a big prestige penalty for destroying a CoT, I believe.