there are multiple reasons to turn things on and off.
One is power savings, so if you're right and the devices still are powered on, these will be minimal.
But other reasons include security (prevention of BlueJacking) or compliance with rules that prevent RF interference (e.g. in hospitals and airplanes). What matters there is that the device turns off the radio and stops transmitting, even if the rest of the device is still powered on.
Also, that things are powered back on after a reboot means nothing, that just means that OS X doesn't modify the BIOS settings that would have to be changed such that the computer would power up in a different state.
Lastly, the LED is turned on when EITHER BT or WiFi are active. I'm not sure how accurate it is under OS X, but if you wanted to know if it's accurate, you'd have to power down BOTH WiFi AND BT for it to go off.
