Those are blank by the manufacturer. Many motherboards have blank spots that weren't used for various reasons. I have one that has a blank spot that could've been a pci-e but they decided not to use that spot.
Yes it is for the onboard video controller and has worked flawlessly for over 2 years without it. I have a heat sink I can put on it with Arctic Silver bond if the winner would like. I've found it unnecessary because I've always used an add in card.