I do not have any figures for frequency of such words, but I can provide a psychological reason for why I believe them to be rare.
Common words are easier to process during communication. If, however, one uses rare words composed of multiple morphemes in unusual ways, the hearer/reader has to actively deconstruct them to get at the meaning. A word like ĉielarko is a compound, but frozen to such a degree that it would be perceived as a single unit. Nobody would really take it apart into ĉiel- and arko to get at the meaning.
Using unusual morpheme combinations is thus hard work for both production and reception, and hence not very common. This applies more to spoken than to written language, as reading is not real-time, so the reader can more easily decode such words. As they show creativity, they would be more likely to be used in literature than in everyday communication.
From my own experience, becoming a more fluent speaker of Esperanto involves picking up common words (esp with affixes) and storing them as single units.