In Gnome, there are two shortcuts, armbian-config and armbian-configNG.

What's the difference?

I assume the armbian-config shortcut is a left-over from the old version of this tool: https://github.com/armbian/config

It has been replaced with https://github.com/armbian/configng

So, i should use armbian-config in terminal and armbian-configNG in Gnome.

I don't know where these shortcuts link to, but I assume they both link to the same executable script which is the next generation version. I am not aware that any current Armbian image still ships the old version. So at the bottom-line there is no difference.