Shop's won't take 50s and 100s for another reason. Almost nobody uses them within the borders of USA. The clerk at the store (often a kid from a high school) just don't know how they are supposed to look. ;-)
50s aren't particularly common, but ATMs in Nevada and Reno disburse all large amounts using Benjamins. They are a pretty common bill. I'm guessing 99% of those clerks in a store would have no trouble recognizing one.