The Romans didn't have computers, so they didn't worry bout using only 3-digit years back then. And today, looking back, using fewer digits than available doesn't cause any problem. There's only an issue going forward, when more digits are needed, which the Long Now is trying to mitigate (8000 years early).
Romans needed many more than 3 "digit" (or rather letter) to represent this date. Also, the AD system (counting the year since the birth of Jesus Christ) was introduced much later.