I guess it could affect the "overall", but if the beer's solid in every other aspect, I don't think most judges would lowball the overall because of clarity. I certainly wouldn't. It's like this, for me at least; I get the beer and the first thing I do is look at it. If it looks right, 3/3. If it's say too hazy, not enough head, etc. 2/3 unless it's terrible. Now say it is a 10a and it's brown, I may give it a 1 or a 0 depending on other aspects of the appearance. After I score "appearance", I go Aroma, Flavor, Mouthfeel, Overall in that order. By the time I get to Overall, unless the Appearance seriously hurts the brew, it's not high on my list of things to mention. If the Appearance is seriously out of whack, I may mention it and knock a point or two in Overall.
Something to consider: I know a lot of judges (myself included) who pretty much know the score they're looking to give early in tasting each beer. They'll then work the math back to that score. The Overall section is a place to make math on a scoresheet. So say your brew's really nice, spot on for the style but a tad too hazy (or lacks head retention or is too pale), you may actually gain a point in Overall, despite losing one in Appearance, if the judges liked your beer and it was otherwise a good example.
Hope that helps. Keep in mind that the vast majority of judges are home brewers, and the vast majority of the beer they judge is home brew. Make a good beer that represents the style category well, don't do anything too outta whack like use Citra in a BoPils, don't sweat the minor stuff (like perfect clarity) too much, and you'll score well. From there you can work the recipe to perfection and hunt out that 48 pointer.