Hello there and thank you for asking :) They look the same but they are not identical twins! There is a short and long story to it :)
Short answer: 1 squirrel has 2 holes and the other has 3 so that what differentiates them. Pepper has more holes because salt is finer ground than pepper. Pepper has more holes, makes it easier to shake it out. Salt is free-flowing, less holes needed.
Longer answer if you are curious about shakers history...
Traditionally, pepper was more expensive than its easier-to-come-by companion salt, and so pepper was placed in the shaker with fewer holes to reduce usage. On the other hand, the International Guild of Professional Butlers asserts that salt shakers generally have larger and fewer holes to accommodate the larger, heavier grains that flow faster than pepper, although they do admit there is no manufacturing standard.
There seem to be two distinct camps in this matter -- the "Flow" camp and the "Flavor" camp. The Flow camp preaches that pepper grains are larger than salt grains and hence need more holes to equalize the flow between the two condiments. But interestedly enough another but similar argument argument reversed them two claiming that salt is coarser than pepper and thus goes in the shaker with more holes. It depends on the types of salt and pepper you are using.
The Flavor camp dictates that since people tend to use more salt than pepper, the salt should go in the shaker with more holes. Of course, if you are one of many people on a salt-restricted diet, this solution may not make sense for you.