I know throwing weapons are mainly used for pulling, but does the damage done by a thrown weapon increase when i put points into that weapon's skill.

For instance, shadowblades cant spec throwing, however they can spec axes, so say i spec axes and im using throwing axes, is the damage higher because i spec'd axes?

I belive, its not. By the crossbow and the Infis, its kinda, you do dmg depending on your level. At level 50, its about 150 dmg per shot, and up to 300 vs. greys, or 100and less vs plate.
But an Armsman can spac crossbows, but he still does between 50 and max-leveldmg dmg. His maxlevel dmg at lvl 50 is about 300, and up to 600 vs greys, then^^. But, his every hit varies between 50 abd 300. By speccing crossbows you cen increase your min. dmg, so, while having 50 crossbows, youll do about 300 dmg per hit vs enemies.

Maybe, this data is incorrect, but thats my experience during playing the game.

thanks, ill have to experiment ^^