Since I was fortunate enough to get the Duke Nukem 3D soundtrack from Retro Music Bundle before it got removed. How come the GOG.com Duke 3D doesn't have the soundtrack? Duke 1 + 2 has it but why not Duke 3D? Will there be one in the future?

Speaking of which, on the atomic edition of Duke 3D game disc, there was an audio track of the Duke Nukem theme. I already have it so it doesn't bother me but I still think that should also be bonus content download.

This could prove as an useful example about soundtracks' rights being tricky.

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.

Perhaps it's because more people than just Bobby Prince were involved in the music? I believe MegaDeath was involved with the theme, so that adds complications.

My suggestion is to find the music amongst the game files, listen on YouTube, or download it another way.

https://www.google.com/#q=duke+nukem+3d+soundtrack