The thing to always remember when it comes to trade is that trade power in itself doesn't matter. What matters is the value of the node, and the share of that value you are actually collecting on. (NB: just because you own 50% of the power, doesn't mean you are collecting on 50% of the value: sometimes your trade power will ultimately feed other countries, and vice versa.) So the ideal is to have a strong node of chain of nodes where you have most of the power and hence can collect everything, but if you can't achieve that, don't waste power on pushing trade between nodes where your share is low. As bly08 says, if you don't have a near-monopoly, it's often better to collect in several places.
Light ship spam is at its most powerful, not in one of your main collection points, but immediately upstream of a node you already dominate. So for instance if you have full control of Sevilla, that's the time to send a fleet to Tunis or Ivory Coast. You have to look at hostile trade power there, versus the extra value you can collect on. The more power it takes to extract a ducat of value, the less worthwhile it is to send ships there.
By the way, leaving Portugal alive but weakened isn't such a bad move. The Portuguese AI will continue to colonize and make CNs, but its weakness will mean it struggles with liberty desire. The AI's response is to frantically develop its CNs to appease them. If you later annex Portugal, you'll inherit the Portuguese CNs, and not only get the benefit of all that extra development, but they'll also be extremely loyal since the LD modifier persists after a change of overlord. So you can potentially pump up the tariffs and make a huge income off the ex-Portuguese CNs without them going disloyal, and without having to develop them yourself. (You should think of tariffs not as stealing your colonies' money, but a mechanism for actually creating money that creates liberty desire as a kind of pollution.)