The cost to manufacture chips is roughly the same regardless of the denomination. There are some economies of scale such that the more chips of a single denomination the manufacturer makes, the cheaper each one is, but those are small effects relative to the basic cost of labor and materials per chip, which are essentially the same no matter what the chip's denomination is.
The reason that fracs and high value chips are more expensive on the hobby market than workhorse chips like ones and fives and twenty-fives is simply that there's fewer of them available, because casinos ordered fewer of them, and so fewer of them made it onto the hobby market. Fewer available means higher prices. Supply and demand.
Edit: Chips with more complicated spot patterns are modestly more expensive to manufacture, because there is extra labor involved in cutting out the inserts (the "spots"), cutting out the holes in the chip blanks where the inserts will go, and placing the inserts into the holes. It's mostly a manual process, hence more complicated spot designs means more labor which means higher cost. Prices on CPC custom chips with complicated spot patterns reflect this extra cost. However, for casino chips that are now on the hobby market, the cost to manufacture the chip is completely unrelated to the price you'll have to pay to convince someone who has a chip you like to sell it to you. That's purely down to availability. Chips today sell for many times what it cost the casinos to buy them from the manufacturer.