Is there a way to make these unofficial expansion packs work with the GOG.com version of DN3D?

Yes. The GOG version just bundles it with DOSBox, so the game itself is just the DOS version. Therefore you should be able to just use DOSBox to run the DOS installers of the expansions.
Alternatively, use eDuke32. It is possible to use just the core game files and the core files of the expansions to get them running, but it takes a little bit of extra work to get the right format files (I had to search for how to do so and it involved using user-made apps to extract the files from the expansion installers).

Thanks for the detailed post!

I wish that Gog would just release these expansions. They're impossible to find these days. :/

Torrents.

I mean legal copies.

I'd be interested, perhaps a forum thread petition would help. But, they may be working on that already, and just not gotten permission. Or possibly are saving it for when Duke Nukem whenever is released.

Couldent the rights to the other expansions be purchased by anouther company?

A company going out of business doesn't mean that nobody owns the rights to their products anymore, though. Someone owns the rights, it's just a matter of finding out who.

SHODANFreeman is rightthe problem is that they weren't official

How do you know they were not official?

They were made with the permission of 3DR as a retail mod but Sunstorm owned the rights to the titles sunstorm also ran Arush who did DNMP. 3DR managed to unstick the rights to MP but has no interest in acquiring and having to support those packs. if the rights holder decides to vacate the rights or decides to re-issue it as freeware maybe 3dr will post a downloadable version like they did for the shadow Warrior level pack sunstorm made and never issued.

If Shadow Warrior ever got a sequel. who would have done it? a man can dream

I dont understand why someone else has the rights to expansions that are from someone else's IP. And yeah SW sequel would be awesome.