The Sakai Tanto is Jin's short blade and his tool for silent kills. It starts as a rope cutter and becomes the assassination weapon in The Warrior's Code, so upgrading it at a Swordsmith is key for a stealth playstyle.
Stay undetected (the enemy's meter must not turn red), get close and press Square. Strikes from above work well because patrols rarely look up. Chain Assassination techniques let you take two or three enemies in a row with Triangle.
Until you earn the Ghost Stance in The Ghost of Yarikawa, stabbing a leader is only a Critical Strike that deals heavy damage. After that you can kill them outright, but only if fully undetected.
Get the tanto to level II early. An unupgraded tanto is slow, and victims can cry out before they die, alerting the camp.