As one who has played the AI fairly extensively, I observe there are a few cards that seem to be very rarely (if ever) used in AI decks. These include:
Fire: catastrophe, inferno
Forest: nobbling elder, faerie enchantress, heart of the forest
Ocean: triton waverider, back to the depths, fluidity
Underearth: darkling schemer, wrong tunnel
Swamp: blood orb, waiting grave, dark secrets
Air: energize, power dive, spell book
Jungle: ravager, pack attack
I know an attempt has been made to expose players to a wide variety of cards and play styles: starter decks usually have many different cards rather than multiple copies of only ten cards, advancement in level allows each region to be defeated only once, decks for different regions of the same faction still have a very different feel, most cards do appear in AI decks, etc. And I know many of these "unused" cards play pivotal roles in some of my favorite decks, so I know they are interesting and useful. Which brings me to my question,
"Why are these cards not used by the AI?"
I conjecture it may be a combination of the following:
a. The cards are used, but I simply didn't notice/encounter them (perhaps the AI has no reason to play them against my decks).
b. The card will be used in later decks (perhaps with cards from an as yet unfinished faction).
c. The AI is not equipped to handle some cards well.
d. These cards often require a special deck design to really be helpful, and there hasn't been space for special, gimmicky designs -- yet.
e. With all the possible cards, and hundreds of AI decks, it was simply not noticed that some cards were not used often.
You are correct, as always – it's a mix of most of those factors.
A few simply required too much messing about with the AI for just a handful of cards. These are the kinds of cards that are even hard for us human players to know when it's best to play them; playing them at a less than optimal time could lead not only disadvantage but utter disaster. For example, Ravager and Catastrophe.
Some of the cards that got added later to the set also didn't get as much use as the 'core' cards, simply because it didn't seem right to retroactively include them in too many older AI decks. In future decks, they will get as much of a look in as any others. For example, Faerie Enchantress.
Some you mention definitely are there though. For example, Triton Waveriders is common in the lower level decks, which is why you might not see it much anymore. There were, at last count 495 AI Decks, so things tend to even out, except for common utility cards that feature heavily to give the AI a fighting chance.