I think what makes the Drake hair so much better than the other games is the occlusion below the hair. You can see this clearly in this shot:-
http://farm4.static.flickr.com/3512/3180426114_c333a0b91e_o.jpg
Compared to something like this MGS shot:-
http://i27.tinypic.com/2dqlsn4.jpg you can see how the fact that the MGS shot has a bright scalp and forehead area, regardless of how much hair is covering the area. I did notice in one shot that there was some slight shadowing down the forehead of Naomi, it looked like a cut-scene shot, which means they may use a different lighting system for cut-scenes. Either that or the piece of hair casting the shadow never animates and they have built the shadow into the texture.
The fact is though, hair isn't transparent and anything underneath should reflect that property. Now they (the Uncharted devs) may have just painted the scalp area darker on the characters to create the illusion of shadow. But which ever method they have used, the added depth and solidity it gives the hair, is a definite plus.
It would appear than despite the many graphical irregularities in Uncharted, they have at least taken the time to deal with the hair and its reaction to light properly. Hopefully, this is something other devs will notice and take the time to make sure their in-game hair looks as good.
I mean, it's all fine and dandy to have great hair textures... but if it looks like some "plonked on" wig, the effect is killed stone dead.