For others playing along at home the NSBMD is the format Nintendo eventually provided for developers to have for 3d models on the DS (which has a basic 3d hardware seup built into it http://problemkaputt.de/gbatek.htm#ds3dvideo
). It is related, somewhat loosely, to the BMD format seen on the gamecube, wii, wii u and 3ds. Tends to be flanked by NSBTX for textures (some of which can be edited in tile viewers, though some have odd formats most tile viewers won't handle and you will want something like tinke) and NSBCA for animations. There are some other formats for texture animations and something else. Not all things use textures (model colours and very basic vertex colours are available in the models themselves to do things) and the NSBMD format itself has limited provisions for having textures within it as well.
Not all devs will use the NSMBD format (indeed I can probably find more examples of this, even ignoring the early games made before it was developed, than I can of devs deviating from the SDAT sound format also provided by Nintendo) so be aware of that one.
If MKDS course modifier and the leaked SDK stuff for the ancient 3ds max versions (and a few other contemporary programs) don't do it for you then you are out of luck and will have to manually edit or create your model, which is a pain though the viewers available should be able to help guide you in and make sure you are not going completely astray. Generally view the model, see what any output is telling you about what things are what, and once you find a node/vertex you want to edit set it to something silly, load it in nsbmdviewer or whatever you are using to make sure you have the right one and then restore and edit accordingly. Unless it is a simple geometric shape I would not go completely from scratch and instead try to find something like what I want and edit it in from there, you do you on that one though -- the DS polygon budget is not so high that you can't keep a general idea of everything that is going on in your head. Naturally you want to be aware of any animations that work of the model as they will tend to be start, middle and end states that might make things look odd if you radically change things or add a load of complexity into the models rather than some kind of relative movement that might make that still be OK even if you make things far larger or are more used to skeletal animations.
I don't know why we never particularly saw DS 3d model editors, or plugins for conventional 3d modelling tools, take off (the 3ds saw such things before hacks became widespread and plenty of systems before and after it saw them) but it is what it is. If you think you can make one (many open source examples of them for other systems already exist and the NSMBD and associated formats are reasonably well understood) then please do share, and you can probably get some people to help you out a bit.