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Its not historical at all. It has its roots there as bolts did not originally exist. However, if you know the nature of materials, wood and steel expand and contract at different rates and sizes. As the seasons and years go on, as you see with older stick framed houses that are poorly put together, the nails work loose, and the rust east through the wood weakening the connection. Wooden pegs, in addition to the joinery, make a wood to wood to wood connection, swelling and contracting at the same rates, if the grain is lined up just right as well, it swells perfectly together, over the years the joint gets tighter instead of looser, and makes for buildings that if odne right can last a millennium. Check it out by seeing how pegged and bolted furniture works out over time.
Another place to look for answers to whether or not the use of wooden pegs are more beneficial than nails, would be to the histories of craftsmanship in building. Look to Russia, where the houses and places of worship were constructed without the use of nails. To the Asian cultures, where wooden pegs were also used and joinery was brought to a very high art. You may also wish to look here in the United States to the Amish, and dwellings constructed before the machine age. Josh is absolutely correct. Ever wonder why furniture of the highest quality is joined with wooden pegs and various joining techniques without the use of nails and screws, and the least expensive furniture is riddled with these things?
Wooden pegs are used in historic construction because nails were unavailable. This type of joinery was phased out in direct correlation to the use of metal fasteners. Mortise and tenon (pegged) construction is superior to standard construction, but requires more skilled labor, making it more expensive. Often, the use of nails replaced pegs when the railroad came through an area. Generally, this type of construction was phased out after the Civil War because of better transportation and more factories making nails. Tcar is correct-the grain of the peg will usually be at a right angle to the grain of the fastened member. Commonly, the holes are slightly offset, allowing the peg to force them tightly together.