I restrict myself to one trade port per trade theatre anyway to give the AI a chance. Not that it usually makes much use of it.
As far as the pirates are concerned, until you can build 5th Rates its not likely that you can take on the pirates unless you are playing the Dutch because the pirates ships are so overpowered in ETW.
What I usually do is monitor the trade theatres and start sending indiamen over once I'm sure the pirates are gone. Sometimes the AI will take them out, but in my current Swedish campaign I've just built a squadron of 5th rates to go and deal with The Ivory Coast (its 1735), and East Indies. But, I've had a full trade fleet in Madagascar since about 1715, because I think the Spanish dealt with the pirates in that zone.
The real problem is that pirates don't behave like pirates in ETW. Instead, they are probably the worlds strongest naval power. All of my largest and most nail biting naval battles have been against the pirates, the AI rarely puts any fleet together even remotely as challenging. Considering what CA could have done with pirates its a bit dissappointing.
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