I do wish the seat was secured by a key lock rather than the allen bolt. Both from a convenience standpoint and also an 'any random passerby carrying an allen wrench can access the internals' standpoint.
Agreed. Once the seat is unlocked and removed from a Kawasaki Ninja, you have access to: Battery, air filter, fuses, toolkit, bolts that hold down the tank, the grab bar, the tail lights, rear fairings, etc.
There's still plenty that can be stripped from the bike without opening the seat, but it does provide a safe and discreet little storage box.
Some people use the seat lock to secure luggage, but if you're worried about that kind of theft, you had better remove the luggage -- I've heard stories of people going after luggage with bolt cutters in broad daylight and getting away with it.