The eye bones are used for eyelid movement. For some reason when Raven ported their SoF2 skeleton over to JO, they removed the eyelid bones (as well as several other facial bones) at compile time. It's quite easy to add them back, but OpenJK (I say OpenJK because it'd be stupid to have a separate project just for a new GLA conversion table) would have to adopt the new GLA and create conversion tables for base JKA/JO rigged models to run off the new GLA which will break nothing. I've done this in a test, but with only converting JKA models as I couldn't put more than 1 table in due to my n00bness.