The emuNAND Tool isnt updated for NN3DS NAND size yet and wont work.
Thankfully i just found a post over at maxconsole that helped me out. Basically I used win32diskimager to image the 4GB µSD that came with NN3DS which i updated to GW3D 9.5 emuNAND before.
Then write that image to my 32GB SD...