That's part of the challenge of playing as a pirate. Here's a technique....once you have leveled up sufficiently pick the flag perk for each nationality before you would others. Make certain also to pick up items to improve your stealth and to begin with your characters stealth high during your character's optional PIRATE perk selection at the very beginning of the game.
These quests give themselves away on the world map because the ship you need to talk to will have green of orange sails. I recommend changing your flag to something like French or Dutch before the encounter and then going into 1st person tactical view to see what flag the ship is flying.
If its an enemy note which nation's flag it is and sail away until you can get over 750-850 yards away. Then the game will allow you to go back to world view...sail far enough away from the ship so that you don't bring it back up in 1st person tactical view again and then go to 1st person alone --- change your flag to match that ships nationality.
Then go back to world view and sail to the colored sail ship again and this time he won't be your enemy. If your stealth isn't good there is still a good chance he will recognize you as a pirate when you get close.
This is the only way I know of to work these quests as a pirate Mate. Bottom line there is no doing them until you level up enough to get stealth and other nations flags....until then don't agree to take the missions.
Good Luck
MK