Is it true that the prefix 超 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, 超 (ちょう) meaning “very” is very colloquial. It is highly unlikely to see it in formal contexts, written or spoken.
However, this does not mean that 超 (also written チョー or ちょー) is not used in written Japanese. See latest search results on Google of "超", "チョー" and "ちょー" (but note that not everything in the results is this usage).
We should also note that while 超- meaning "very" is colloquial, 超- meaning "super" or "above" (the "original" meaning of the kanji) is entirely acceptable as a prefix in a literary work. In fact, many words rely on it:
大国 is a word in its own right - 超- is just a prefix.
This answer was kind of an addendum, but has been upvoted a bit (thanks!). I still agree with Tsuyoshi Ito's answer of "no you shouldn't use it in written works" as long as we're talking about the OP's meaning of "very".