Anyone who has worked with pencil knows that graphite is reflective and hence could easily blend into a surface under light. The lines were added, but only to the saucer, when the 11 footer was modified after WNMHGB for series production. Roddenberry is the one who wanted the lines to help give viewers a sense of scale. Didn't really work out since the lines were effectively invisible on '60's era low-res television. He'll, they're barely visible on DVD. But GR wanted them even over Matt Jefferies' objections.
Pencil was used because it would have been too costly and time consuming to have the lines engraved because it would have meant also reprinting and redoing all the saucer's details. And notice the rough nature of the three engraved concentric rings under the saucer.
The 11 footer wasn't a display model that could withstand up-close scrutiny. It was a filming prop that only needed to pass muster on low-res CRT screens, and that it did.
The engraved lines on the 1/350 kit are not as fine as R2 had hoped for, but neither are they as obtrusive as some make them out to be. If someone wants them totally gone for a smooth looking saucer than all it takes is some putty and sanding and paint and they're gone---nothing a decent modeller can't do.
Interestingly Gary Kerr addresses this very issue in the current issue of Sci-Fi and Fantasy Modeller
#28. He has quite a lot to say about it.
Personally I've never liked the lines, but I can't deny that they were there. The best I can do, and still remain accurate, is minimize them.