The music is even better in context. "Where does the Ocean Go?" in particular is set up in such a way that even if you didn't care for the track before, you can appreciate it for what it does.
Chrono: There are two types of fansub groups: the semi-legit, stops when a series is licensed kind, and the need-a-fix-so-badly, we have to sub it kind. Sometimes one splinters into the other. Sometimes there are extenuating circumstances (like One Piece). I can't easily condemn either one because I want to know what happens too!
In the case of a high profile license like GITS, Bandai probably made their wishes known to the fansub groups of the time. The "underground" groups picked things up and ran with it themselves.