You don't mention which version of GTK your using but with Ubuntu 12.04, I'll assume it's gtk+3 because it's available from synaptic in that version of Ubuntu.
1) Don't use hbox, it been deprecated since gtk version 3.2http://developer.gnome.org/gtk3/stable/GtkHBox.html#gtk-hbox-new
2) You can use gtk_box_new() with orientation set to GTK_ORIENTATION_HORIZONTAL. But even GtkBox is going away eventually so you should use GtkGrid instead.
(The manual only mentions this in the documentation for GtkVBox)http://developer.gnome.org/gtk3/stable/GtkVBox.html#GtkVBox.description
3) You don't actually embed a terminal in a GtkWindow. Instead use a GtkTextView widget to simulate it. You launch a terminal as a background process and communicate with it using pipes and one of the g_spawn() functions.http://www.gtkforums.com/viewtopic.php?t=3818http://developer.gnome.org/glib/stable/glib-Spawning-Processes.html#g-spawn-command-line-sync
4) To keep it simple I would have a "SEND" button to transmit what you've typed in the GtkTextView to the terminal. That way you avoid writing keypress code to capture the "ENTER" key.
As far a Nautilus I'm not shure.