Meh, I just took it as a more detailed version of their weakened states. I figure if they hadn't been told to axe the Hyper forms, the cracks would just somehow be repaired when they're powered up.
It's just me or i found that it's really clear by S3&K cutsceens and gameplay that the Super Emeralds are Chaos powered up? They are transformed the first time you go to Hidden Palace and you lose the ability to go Super the moment it happens. (Excluding Doomsday, i guess, but that more not to be too unfair to the player more than anything else). Also i remember someone from the Mania team stating somewhere the ones in their game are just decorative props (lore-wise)
Which, unpopular opinion, I'm cool with. I never really cared for the Hyper forms from a lore and aesthetic perspective. This isn't Dragon Ball, we don't need a hundred million variants of the Super Sonic form. And I always thought the sparks constantly emanating from Hyper Sonic was a little too over the top. And a rainbow-colored form is just flat-out less cool than a gold one.
That would be actually kind of cool if done right... Just imagine if, after getting all the regular emeralds, you could choose one of the Super Emeralds in order to give a colored Super Sonic certain special abilities. Then Hyper Sonic would unlock in the end if you used all of them or something.
Super Sonic 2, Super Sonic 3, Super Sonic 4, Super Sonic God, Super Sonic God Super Sonic aka Super Sonic Blue, and Ultra Sonic.