Quick heads-up: Neocortical nanites are Soft Nanites, not Hard. The second table of nanites (on page 150) is incorrectly labeled as "Hard Nanoware Systems" when it should be "Soft ..." you can see this from the description listings (page 149 is the start of the Soft Nanoware Systems).
Now to answer the question, Mirikon already beat me to it while I was writing, but I think I add some extra detail:
In part, it is about game balance, buying the Nanohive is about being able to maintain the nanites "indefinitely" instead of them degrading over time. It isn't about being able to pay for a lower rating and get free upgrade. Essentially, nanohives are about preventing and repairing nanite colony degredation, not building up something that wasn't there in the first place.
A simple explanation could be that buying a nanite colony at a higher rating doesn't just mean you bought more nanites. Sure that's probably part of it, but not all of it. I don't think they call it out in the rules, but I don't think you can manually replenish a nanite colony by just injecting yourself with more of the same type of nanites. Injecting a new set would probably function as an independent colony (congrats, you have 2 colonies of Rating 1 nanites). So part of buying the higher Rating is also paying for that particular colony's ability to function at that Rating.
Does that help bridge the logic?