There are a couple of ways to deal with this:
1. You can override the colors that NodeXL uses for Categories. Select the Groups worksheet using the tabs at the lower-left corner of the Excel window, then fill in the Vertex Color column on the Groups worksheet using the colors you prefer.
(Categories are one type of Group; that's why the colors are set on the Groups worksheet.)
2. Change the graph's background color to something with more contrast, perhaps a dark gray. You can do this by clicking Options at the top of the graph pane and clicking the Background button in the Options dialog box.