Other than the tool mentioned (which is sketchy) and the old leaked part of the SDK, which requires equally ancient versions of the 3d modellers it was compatible with, most things I have seen have been all about extraction, or maybe messing with textures.
Don't think I have seen anything for proper conversion back to NSBMD, or the option to open one in an editor and play around a bit. They exist for systems older and newer but not for the DS that I am aware of.
If I am ever doing things I usually just edit them raw (I mostly only want to lose protrusions, tweak things slightly so or demonstrate how to do it) after figuring out where the stuff I want is located.
There is a fairly good understanding of the NSBMD format, and probably some nice examples of open source plugins for things like Blender on the 3ds which also has a similar format (though their BMD is closer to the gamecube and wii stuff than what the DS ended up with) if you want to go that way.
, also has it's advantages 
