But the Duke Nukem II soundtrack is still available as a bonus for Duke Nukem I & II on GOG.com but not 3D. I hate it when things get into legal limbo.
Those soundtracks that got removed have been composed by Bobby Prince. Surprisingly DN II & Realms of Chaos, and that lone music track from Catacombs that he composed is still available a bonuses. But I also forgot to mention that the Blake Stone duology and the Unreal Series still don't have their soundtracks as bonuses. :-/
But as you said, things get into legal limbos and with soundtracks, it happens very often. For example, Carmageddon 2 soundtrack cannot be provided through gog because of an Iron Maiden track. All it takes is one artist complaining or demanding a cut of the cake, to send all to hell.
Another example is Hitman Contracts: the soundtrack caused so much trouble that the game cannot be selled through steam.
So, no matter how hard gog tries, some jewels shall never be complete due to stupid copyright technicisms.
At least, legally.