On a scoresheet, carbonation falls under "mouthfeel" category. That's only 5 points out of 50, and there are several factors for mouthfeel, like Warmth, creaminess, astringency, and body, not just carbonation. A good judge will only ding you a few points, maybe 2 or 3 for over carbonated beer. More important is the aroma, flavor, and over all impression. If you are accurate on these points, you should score fairly well.
However, carbonation does affect other qualities, like body and hop aroma.
But, carbonation only matters for a few points. You may not take gold for an over-carbonated beer, but if it is brewed well, and to style, you should score well.