To make it work I had to (with the old version) set export GI_TYPELIB_PATH="$HOME/.guix-profile/lib/girepository-1.0"
As far as I know, 'Agg' can only be used to generate files. It can't be used interactively a la MATLAB. That's the reason for including the 'GTK3Agg' backend. Regards, Fede