If a pin has ESD diodes they are connected internally to VCC. So you have a path from the pin to VCC through a diode. Therefore if you apply 5v to the pin you will get ~4.5v on VCC and the chip will happily work.
As you say unless you have a battery-powered system the extra current probably doesn't matter, but it's generally considered bad form to power a chip like this. It may draw too much from the AVR pin although with modern chips probably not and anyway the diode would blow first I think.
But there are other issues, the chip is running with nothing plugged into some of its inputs so they are floating, That's never good.
Rob