This is a difficult one to answer.
The best answer is RAW: you must pay the full cost. This is because cracked stones should be the result of improperly trying to create one (similar to cursed items), and broken are from damage. This also takes into account that broken (and possibly cracked) stones can be repaired to make them fully functional. So if you made a cheaper cracked or broken stone, you could just repair it to get the better stone and have paid a lower overall cost.
However since you could start with an already cracked or broken stone as the crafting component, which will directly influence the end result an argument could be made. You could speak with your GM and see if they will allow you to craft the broken one, say its the base ioun stone itself which is the expensive component for the crafting, so by getting a broken one you save yourself that money. It could also be considered that cracked and broken stones cant be used at the start of crafting and are thus fully a result of incorrect procedures. In this case I would not allow it to be repaired to become a fully functional stone, or increase the repair price to make up the difference.