I can only speak to what I apply in my own work. I'm sure others will disagree. It's my understanding that almost without exception, every component of wood that is used in acoustic instrument building should be quarter sawn, including necks. It have more to do with wood movement than it does strength. A quarter sawn board of any given dimension will shrink a lot less across it's width than it's flat sawn counter part. Can you imagine a quarter sawn neck mated to a flat sawn fret board? Chances are you're going to have some movement between the two pieces before long and develop a nasty ridge where the two pieces meet....or even worse. Some people also believe that quarter sawn braces are stronger because of their vertical grain orientation but simple testing proves that notion wrong. Quarter sawn braces are also much easier to carve! Aesthetically speaking, flat sawn pieces cannot be properly book matched for body construction, aside from the shrinkage problem.
Having said this, when you order a guitar neck blank from StewMac, you have your choice between flat or quarter sawn. Beats me why. Oh, and electric guitar builders seem to break most of these "rules" just because they are a squirrely bunch.....
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