If you shoten those wires/leads you have to get a new Futaba, sanwa, hitec plugs etc. Because if you re-use those it will be loose.
I don't see any harm on shortening your wires I've tired it and I didn't notice any drop in performance.
Also one way to make your electronics wiring nice and neat is used a black shrink tubing this way you don't have to cut those wires.