If the shot lands close enough to them, they will move to investigate it.
If you're struggling to find places to kill certain bodyguards or targets where they won't be found, I'll offer some suggestions below, but keep in mind that you can always lead them to certain spots with a series of shots. A lot of my witnessed kills came from missing a shot, drawing attention to that spot, or hitting guards successfully while they were in motion, but being too focused on their movements to notice nearby witnesses. Headshots are also not necessary but I went for them anyway - if they were still enough for a headshot, I felt much safer about taking them out. You can have kills noticed as long as you are able to take out the witnesses as well before they can raise an alarm (as long as the witness in question is another target) - make sure you get the "Situation Contained" notification. This means you must hide most bodies where they cannot be found with the only exceptions being bodies which will fall where no one else is patrolling. You must kill all your targets, not kill any civilians, and not have any alarms raised. In order to receive it, you must essentially play the level flawlessly. Silent Assassin is a rating you can receive for your performance on missions. Nothing wrong with the video guide already posted, but if you're like me, you want to know exactly what the requirements are in case you can't perfectly mimic the guide.