This happened to me on my 3DS without Gateway installed. Miiverse crashes if I try to launch it but it is there. I posted the thread a while ago.
Restoring 6.3 image and re-doing system update successfully first time fixed it for me, eShop and Miiverse are now working fine. You should restore an image or start the EmuNAND over (backup your saves on the SD card first ofc) and try again :0
Oh wait, unless you mean SysNAND, not sure what you can do then :/













