I think thats the only advantage of a 3D capable NMT...
Being able to play 3D iso, BDMV, Full Frame Packed/MVC files. If you are only playing side-by-side and top-and-bottom 3D files, non-3D nmt will be ok as long as your display is 3D capable.
But based from reviews, 3D iso, bdmv and full frame packed files have better quality / 3D depth.