If you are behind cover in stealth mode, as soon as you pull the bow you pop-up from and become momentarily more visible, but the instant you release you pop back down again, taking cover. Hitting anything with a bow shot from stealth mode also multiplies the impact by a lot.

By keeping an eye n the the little eye-con, you can tell how visible you are. Making noise defeats stealth, as does moving when your quarry is looking your way.