Okay,
@bakterio, here is what you do:
Grab my alpha build of GodMode9 from here:
http://workupload.com/file/lqZrdozu
(Don't write anything to or delete anything from your SysNAND!)
Enter this folder in EmuNAND CTRNAND (4

:
4:/title/00040010/00022300
In this folder, delete the first .tmd file you find. Now reboot to your EmuNAND. Does H&S still work? If not, restore your EmuNAND backup and try again with the second, then with the third and so on. In the end, you should have deleted all tmds that have no effect on the system, meaning only one tmd will stay.
After you have done this, inject H&S -> working!