There are a couple of things that you are rewarded with for finding all 30 crystal skulls, but none are a new weapon. Here is what you get:

1. Three achievements: Karma of the Warrior, Karma of the Mentor, and Karma of the Master Ninja. All are 20g.
2. A gamer pic: It looks like the picture for the achievements.
3. The ability to collect the Giant Crystal Skull in Chapter 13.

Collecting all of the Crystal Skulls and the giant crystal skull will give you a large boost to your score by giving you a karma bonus each time you kill an enemy.
Source(s):
Ninja Gaiden 2 FAQ
http://www.gamefaqs.com/boards/genmessage.php?board=943273&topic=453956...

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