Sorry I've never played either of them didn't realize there was a difference.
There's an ancient DS source branch belonging to the Doom64ex project. I guess the community really wasn't interested in DS homebrew at the time and svkaiser - the projects maintainer - silently moved on. The desktop versions are fine though. In a very old devkitpro thread, we actually see doom64ex running on DS hardware. However currently, upon building against the latest devkitARM, Doom64ex almost immediately crashes.
I think most of the heavy-lifting has already been done by svkaiser. In fact, I think he actually mentions that the game is fully playable on the hardware. Seeing this running at 60fps and in 3D would be a treat.

