1. Does using 3D instead of 2AA reduce the operating temperature?
3 cells (D or AA) may result in slightly better boost efficiency, but the chip will still get very warm if it is charging at 500mA.
2. Regarding shorting two pins to reduce the current draw. I've heard that it fools the device into thinking that it's charging from a computer usb source rather than a wall charger. Does that reduce the operating temp?
Actually it is the other way around. A computer USB port can't have shorted pins because it needs them to transfer data. The USB charging standard calls for shorting D+ & D- to indicate a DCP or Dedicated Charging Port. Implementation varies, but most current generation devices seem to charge OK at the MintyBoost's rated 500mA rate with the pins shorted.