Had this in my notepad from a while go, does the trick.
NNID is listed in: \data\<your unique id>\sysdata\00010038 > 00000000
It was pretty simple to do it and here it is how i did it:
1. I extracted my fat16 xorpad using launcher.dat from 3DS_Multi_Decryptor
2. Dumped emuNAND.bin using emuNANDTool
3. Extracted emunand.fat16.bin
4. xor'ed emunand.fat16.bin
5. Mounted emunand.fat16.bin.out with WinImage
6. Browsed to \data\<your unique id>\sysdata\00010038
7. Deleted 00000000
8. Renamed emunand.fat16.bin.out to test.bin
9. xor'ed test.bin
10. Injected test.bin.out into emunand.fat16.bin with HxD
11. Injected emunand.fat16.bin @ offset B930000 with HxD
12. Injected my new emunand.fat16.bin into my SD Card using emuNANDTool
Eh, voila, after booting into emuNAND NNID was gone