That's a tough call.
You can touch up the black on most marquees without problem.
The black is designed to be opaque, and anything opaque that covers the holes won't show.
The colors are designed to be translucent.
What you need to decide is whether the white spot in the color bothers you more, or less, than having a darker green spot there would.
Even if you match the COLOR exactly, you will never match the thickness of the ink.
If you don't have EXACTLY the same thickness of ink everywhere, it will be darker than the surrounding area when backlit.
Most of the backlit marquees are actually flood printed with white after the ink is applied, as well.
This layer serves to diffuse the light coming through, and prevent the more tranparent colors from having hotspots in them.