During the Seven Years' War, there were three factions of bounty hunters. Assassin-affiliated bounty hunters targeted ships that attacked French ships. The other two factions were the British and French bounty hunters. These two factions targeted criminals that terrorized British and French territories respectively.
Bounty Hunters are probably the most formidable enemies that could be fought in the game and there is no way that Shay could break their defense and could deal high damage to him. They can be killed by using Rope Darts, firearms or by shooting a berserk dart.