After installation I opened "music" folder and did not found one of my two favorites track from the game.

This is the one -> http://www.youtube.com/watch?v=T6jT4uCcQGw

Is it missing in the GOG edition or just buried within other files? I can't see any other tracks in the game's config menu either.

Have you checked the DOS and the Windows version?

I was referring to Windows version in the first post.

Now I checked DOS version and it's the same situation within the game but the music folder contains other .WD files. Don't know exactly what's in them...

The soundtrack available from GOG separately includes this track so it kinda looks like they missed it in the game.

Shame on you, GOG.