From Wikipedia:

“A "dozen" is a unit of measurement. It means twelve (12) items of something. The term goes back to duodecim, which means 12 in Latin. Humans might have started to count on a base 12 because there are approximately 12 cycles of the moon in one cycle of the sun. In other words, a solar year has 12 months. The first to have used the unit were probably the Mesopotamians.

12 dozen (144 items) are a gross. 12 gross (1728 items) are called a great gross. A great hundred is 120 or ten dozen (a dozen for each finger on both hands).

The dozen is convenient because its multipliers and multiples are convenient: 12 = 3 × 2 × 2, and 360 = 30 × 12. The French word douzaine means "about twelve" and is part of a family of words with similar meanings, e.g. vingtaine – "about 20" centaine – "about 100" etc. A baker's dozen, also known as a long dozen, is thirteen.”

So, as you can see, the idea of a dozen seems to be deeply ingrained in our history and psychology to the point that we probably shouldn’t question it too much and leave bakers to ponder the mystery of 12=13.