In In Nomine, a navy can prevent pirates from spawning by patrolling. In contrast, HTTT allows even docked ships to exert control over a range of sea provinces, thus greatly reducing the appearance of pirate fleets. This was implemented after many players complained about the amount of micromanagement required to deal with pirates.
Disabling Pirates completely in Heir to the Throne is a bit more complicated than before. It is not possible to remove the pirates without also removing the blockade feature and some associated missions.
Find the file common\technologies\naval.txt within the game folder. Before making any changes, back up this file, or you risk messing up your installation! Find where it says "blockade=yes" and delete this piece of text.
This will cause all blockades (including yours) to disappear. You must then go into the missions folder and in during_war.txt file and delete all missions about blockades, (break blockade and make blockade).
This should cause no more pirates to spawn in your games.
To remove pirates from In Nomine 3.2, open common\countries.txt and comment out the line for the Pirate nation (PIR) like this:
#PIR = "countries/pirates.txt"
To remove pirates from your current game, locate the "PIR=" section in your save game and remove it completely. Starting with "PIR=" delete everything until you get to the native nation, "NAT=". If your game has been going on a long time, this could be a rather large section.
To remove pirates from In Nomine 3.1, go to the history\countries\pirates.txt file and change their technology group to new_world