I just had hand-scaped hardwoods installed & they did the scaping after the wood was nailed down. I realize it's supposed to look distressed - but some boards have small chunks missing while others are only mildly scaped. I'm concerned that water could get under the wood or that I may have problems with the areas that are more distressed than others. Is it normal for some boards to look so different? My builder keeps looking at me like I'm crazy and says that replacing random boards will look worse and cause more problems. Is he telling the truth?

IMO, when one buys distressed or scraped floors, you risk them not being exactly as you had in mind. But degrees of distressing is so subjective, no one can know exactly what you think looks right. I completed a large scraped job recently and even though sample boards were made and signed off, I'd say 50% of the floor boards didn't exactly match the samples. What are you going to do? Literally stand there and select and approve each board before it's installed? Some accept your floors as they are. I think your builder is correct. Oftentimes, the more you "fiddle" with a floor, the worse things become. BTW, water shouldn't be a problem if you don't get the floors real wet. It's not boat decking.