Yeah they did, so even if they weren't able to add them into Mania there is a chance that they might come back in a sequel or something.Apparently they made a cameo in Sonic Mania though.
The running theory about the Super Emeralds is that they exist but the events of Sonic 3 & Knuckles didn't happen in canon so they were never powered up and Sonic never turned into Hyper Sonic so yeah.
It shouldn't matter anyways cuz Mania is a whole new continuity that was created after Generations or something, that and Sonic's continuity as a whole is all fucky so I don't know why they couldn't use the Hyper forms, it's just some random arbitrary thing that Sega did.