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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.
The number of holes in the grinder plate will vary by the diameter of the plate, so basically the larger the plate the more holes the plate can have. Example: 3/4 plate for a #10/12 grinder will have 5 holes while a #22 grinder plate will have 6 holes.