My experience has been that saddles have the most important effect on tone, nuts have less but it's still discernible, and bridge pins have the least effect of all, unless you add substantial mass to the bridge by using brass pins.
So, yes, I do think nut material makes a difference, but it's subtle. And, yes, I tend to prefer bone nuts.
My usual routine when dialing in the sound of a new guitar has been to replace any synthetic nut and saddle materials with bone. On more than one occasion I haven't liked the effect of the new bone saddle, so I have switched back to the stock saddle or even tried something different, like the micarta saddle that seems to sound best on my recently acquired Gibson J-60.
But I have never once gone back to a stock nut made of synthetic materials. Bone seems to be the best material for that part, at least in my experience. So what I suggest you do, Rex, is get a bone nut made and installed, but keep the original nut, as well. In the unlikely event that you don't like the bone nut, you can always go back to the one that came on the guitar.
Hope this helps.
Wade Hampton Miller
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