It was because if something cost 9.99 and the customer gave a 10 dollar note, he would have to open the register to return a penny instead of pocketing the bill

It was because if something cost 9.99 and the customer gave a 10 dollar note, he would have to open the register to return a penny instead of pocketing the bill. It's also the reason those cash registers made a loud ding when they opened.