I can see them just fine as well, but that might be a monitor thing, or even a color vision thing. Red/green is the common issue, but people seem to have all kinds of issues, diagnosed or not.
As you are well aware, I will whip up a mod if I think something needs changing or improving, but I have never had a reason to mod the oil shale deposit color on the maps. They stand out fairly well against the yellow biome color.
Are they the little purpley spots? I don't mine oil shale often enough to remember what color they are, but I know when I did the Desert badge the first time after 2.0, I had trouble finding oil shale.