Is 超 (chō) seldom used in written works? Is it true that the prefix to mean “very” is seldom used in written works (like novels, not counting direct speech), and is usually only used when talking?

It depends on what kind of written works you consider.

As Boaz wrote in a comment on the question, () meaning “very” is very colloquial. It is highly unlikely to see it in formal contexts, written or spoken.

However, this does not mean that (also written or ) is not used in written Japanese. See latest search results on Google of "", "" and "" (but note that not everything in the results is this usage).