This sounds all very strange. Have you checked for broken packages?
You are on GNOME, so nautilus is set as default file browser.
That's what the command xdg-mime query default inode/directory
is checking.
If you wanna go with nemo, you should set nemo as default file browser. This might solve the Telegram/WhatsApp issue, since they probably try to open what is set as default file browser.
You set default file browser with:
xdg-mime default org.gnome.Nautilus.desktop inode/directory
In this case, it sets nautilus. To set nemo, replace org.gnome.Nautilus.desktop
with the name of nemo desktop file you find in /usr/share/applications/
Also I had read somewhere about a GNOME 47 nautilus bug. If I remember right, it was wayland related. You could try to boot in X11 session to check if it makes a difference.