Oh man, I finally found the part where the theme originated that's used when looking at the Hermocrates. Turns out, in the rip the cue is called Let There Be Light, which plays when Indy dives for Atlantis and manages to turn on the lights.
So, is this really the Hermocrates theme? Because the book actually re-uses two themes from other parts of the game. I guess this could simply be called the Atlantis theme, because a variation of it can also be heard during Sophia's presentation, plus the Hermocrates discusses Atlantis as well.
This cue puts a lot more weight behind the theme, making it much more important. Very fittingly, since Indy FINALLY sets foot in the lost city.