I wasted so much money on the trading game for such little return. I recently lost about 12k due to pirates attacking my ships near Seville. I think it's safe to say the vast majority of crafting/mini games in AC are pointless.
I haven't tested it, but a later Pirates mission has you steal the blueprints to a cannon design that's supposed to be more effective against pirates.
Maybe that helps lower the chances of a pirate attack.