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I believe that with the new salt and pepper shakers, the salt shaker is the one with 3 holes, while the pepper goes in the one with 2 holes. Salt is used more than pepper anyway. Pepper should only ever be fresh ground at the table, meaning salt shakers win out.
Therefore, the salt shaker should have more holes in order to improve the flow, while a pepper shaker should do all right with fewer holes. Others say that it's not the number of holes that makes a difference, it's the size of said holes. Salt grains are thought to be larger than equivalent ground pepper flakes, so they should be put in a shaker with fewer, but larger, holes.