Usage of noxious, nocuous and their opposites

Solution 1:

Innoxious is used in medical, chemical, and certain manufacturing fields to mean that a substance is not injurious, hurtful, or damaging, especially to tissues. Do a Google search for "innoxious medical" and you get 768,000 results. Of course innoxious is the antonym of noxious and a synonym for innocuous. (Those three words appear in Dorland's Illustrated Medical Dictionary, 30th Ed. Nocuous, however, did not merit an entry.) Both Dorland's and Saunders Comprehensive Veterinary Dictionary include in their definitions of noxious the word "pernicious," which in medical dictionaries is defined as "tending to a fatal tissue." That is, something that is noxious can be very damaging to tissues, irreparably so.

So to answer your question, the most commonly used words (as you suspected) are innocuous and noxious. Innoxious has use in certain fields. Nocuous is just not used.

Solution 2:

An interesting question: I didn't know that there were such words as nocuous and innoxious. I'd suggest the answer would be that very few people have heard of these words, and therefore noxious and innocuous would be preferable.