Hum... I never accessed eshop while in sysNAND in my new 3ds too. Is it because my nands (emu [rx-e 9.0.0-20U] and sys [9.0.0-20U]) are unlinked (or maybe not, please read the edit part, hehehe)?
Or maybe because my emuNAND still in 9.0?
Edit: I am not sure if my nands aren't linked after reading the thread
https://gbatemp.net/threads/tutoria...ncluding-emunand-coldboot-cia-manager.405589/
"What you want to do now is unlink NANDs and that's easy. Go to System Settings, other settings, scroll to the last page and choose Format System Memory. If there's a prompt asking you to connect to the internet, do it, don't worry, there'll be no update. When the warnings show up asking you if you really want to format the device, take out your microSD card. Don't forget to do that or you can repeat everything up to now. Then format the device and reboot. During reboot, put your microSD back in again and follow the instructions to set up your N3DS. Now your NANDs are unlinked and inside the \Nintendo 3DS folder on your microSD should now be two folders with letters and numbers. This is the proof that your NANDs are unlinked. "
But I have two folders with letters and numbers and another more called "Private"