The BG1 helmet animations are leftovers from BG1, and the skeleton animations from BG1 are re-used in BG2. The playable races, however--humans, elves, dwarves, halflings--use new animations. They can face 16 directions, not just 8 like in BG1, and have different armour/weapon animations to go along with them.
Oh, and the way that a skeleton and a human using the exact same helmet can have two different animations is the same way a halfling can use the exact same helmet and not have it appear floating two feet above his head. In the helmet item file, it's given an animation ID such as H1 or H2 or something. The game knows to use animation BLAH for humans, BLOH for skeletons, and BLEH for halflings. The halfling and human animations are the same, though, just at different coordinates (the head). The skeletons is totally different, though.