I am going to report my experiment with xfce4 4.2.
In the akita.xmodmap, the number keys section is commented off. I first remove those !'s and activated the section. If you start xfce4 with this section activated, xev will distinguish 3 and Fn+3 - it actually recognizes Fn+3 as "F3". If you press Fn+3 in the windows manager, you can create a shortcut with "F3".
However, it seems like xfce4 window manager(which is in charge of the shortcuts, I guess) does not distinguish "3" and "F3". So, the shortcut gets fired whenever you press "3", as well as "Fn+3".
With the function keys enabled(i.e. the number key section commented out), if you press "3" in LeafPad you get "3" on the screen. If you press "Fn+3" nothing happens. If you press "Fn+1", it brings up the "about" dialog which is connected to the shortcut "F1". However, the same thing happens with "1", which makes me believe that xfce4 is not distinguishing those two different inputs.
Any chance this is a bug in xfce4's shortcut routine?