Literate and illiterate we strictly use for language and reading.
I understand your question, but the answer is too complicated. I think we use about three words for what you use, and attached to different subjects of knowledge. One of those words would have to be translated as:"have a good grounding in"- onderlegd
scientifically literate - wetenschappelijk onderlegd.

The second part of your post is not very clear to me.