My 4Runner didn't originally have a navigation from the factory. So to install my Toyota navigation unit, I had to tap into the reverse and speed sensor wires under the dash. Since you already have a factory-installed navigation unit, this is already done for you.
The speed sensor works along with the GPS signal to track your vehicle at all times. In fact, your navigation system uses the speed sensor almost continuously to track your vehicle's movement, and really only uses the GPS satellite tracking occasionally to make corrections. Portable GPS units don't usually tap into any vehicle wiring, so they rely 100% on GPS to track.
A good example of this is when you're going through an area without a signal, but still see your vehicle moving on the screen. When I drive through the Lincoln Tunnel (which is a very long tunnel, just in case you didn't know), I see my movement tracked all the way through to the very end, even though I'm not receiving a signal. With a portable navi, I would lose the signal as I enter the tunnel and the screen stays frozen until I exit the other end. So that's the reason for having the speed sensor hooked up and functioning.