I don't think it's possible to give a definitive date for the beginning of the practice of blackening yards. Black yards certainly were common, in naval vessels at least, by the middle of the eighteenth century. I suspect the practice was introduced considerably earlier - and there certainly were ships later than the mid-eighteenth century that didn't have black yards. It's kind of hard to be definitive about earlier periods because the principal sources are contemporary paintings and models. A good marine artist might show an object that was black in real life as grey or brown, because he rarely used pure black paint. And he might show all the spars of his ship in silhouette against the sky. Old models can also be misleading; many of them are unpainted, irrespective of what the colors of the real ships were.
All the yards of the Cutty Sark, according to the very detailed plans by George Campbell, are black. William Crothers, in his superb book The American Clipper Ship, compiled a table of all the information he could find regarding the paint schemes of the ship. In many cases he was able to find little or no information about a ship's color scheme. But there was one consistent feature of Crothers' data: in every document that mentioned the color of an American clipper ship's yards, the color was black.
Mr. Campbell, in his book China Tea Clippers, offers the following rather interesting comments about that type of ship: "In other schemes masts and spars were all white, pale pink, light buff or completely black. Paintings or models which show yardarms only (that is, the outer extremity [of the yards]) as white on a natural wood or black spar, are not authentic. This question was raised many years ago, when men who lived through the tea clipper era were still alive, and they denied ever seeing such a painting scheme, nor do any contemporary paintings or models show it."
If I were building a model of any sailing ship prior to the twentieth century (when white, yellow ochre, and "salmon buff" became common colors for spars), I would (a) search for any available contemporary info about the colors of the yards, and (b) if I came up empty, probably paint them black.
Youth, talent, hard work, and enthusiasm are no match for old age and treachery.