What does the ninja icon mean?

Solution 1:

It indicates that you got a bonus (or better) pick-up from performing a stealth kill.

Solution 2:

You get a slight bonus in ammunition gained when you pick up an item with the mask because you've killed someone with a stealth kill.

http://www.gamefaqs.com/ps3/955125-uncharted-2-among-thieves/answers?qid=118819

Solution 3:

In Uncharted 2, I believe it meant extra ammo because of a stealth kill.

In Uncharted 3, it means that you get a better than average weapon for a stealth kill. If you look closely, when the enemy is alive he may have a Arm micro or Ak-47, but when you ninja him (stealth kill) he may drop a tau, T-bolt, or an explosive of some sort. In some cases it's just a grenade so you can't really tell the difference.