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I just received my 2016 LP Junior (satin finish) and there is a small crack near the nut.
Would like to know your opinion on this : is this structural, or only cosmetic?
Looks like a score mark, not a crack. I’d resist the urge to do anything at all. It looks very minor and being dark coloured it’s hardly noticeable. Just play it.
I would leave it be. Think of it as a ‘beauty mark’ that is unique for your guitar.
If you try to polish it away, you can easily polish away that thin finish and be looking at the bare/polished wood. Then you have an additional problem..unlike maple, mahogany needs a finish coating to protect it from absorbing the moisture from your hands.
You were right, it was only a scratch, probably from cutting the nut at the factory.
I smoothed it with some 000 steel wool and it's almost indistinguishable now.