I have a different take on why I don't use stencil. My thinking is that the paint that goes over my string would somehow adversely affect playability. For instance, some strings are made rough on the surface to have a greater spin potential, so wouldn't the paint/ink reduce that spin potential? If I were using natural gut, I would want the bare "gut" doing its "magic" on the ball, without any interference from the stencil paint/ink.
But then I see the pros do it, and it makes me think that the stencil must not affect the performance too much for them to risk winning, despite getting paid to have a logo on their string.