no idea how to totally remove it. But if you turn down your volume all the way before shut down, make sure no speakers or headphones are attached when you turn it down, then it wont make the beep next time.
Ever since I upgraded my 2009 Mac Pro to the 5.1 firmware and 6 core CPU I have to use Audio Midi Setup to control the volume of my start up chime, the Audio Preference Panel only seems to work with Apps and has no control for the start up chime.