In about 20 rifts, and those are all that I've encountered so far, none will link to another rift. I've played with Thaumic Augmentation before and it did work back then.
By forcing myself into the emptiness dimension by altering my player's current dimension ID, I am able to enter the emptiness. None of the rifts there connect either.

Could someone verify rift linking has not accidentally broken between updates?

I just gave some fractures a try in the latest version, and they all worked for me. Since they were all ones you encountered so far, my best guess about what happened is that you added/removed one of the following mods, which are possible fracture destinations in the default config:

• Twilight Forest
• Atum 2
• The Betweenlands
• Lost Cities
• Erebus
• Wizardry

If this isn't the case, please post a log from when you tried to enter some of the broken fractures. Also, if you need to quickly change dimensions for testing purposes, you can use /forge setdimension <username> <dim ID> if cheats are enabled.

The issue appears to be with Cubic Chunks. I had (I think) both mods working together at some point, with functional fractures. I would have to narrow down the Cubic Chunks update that broke this.

Let me know if you find the update that changed this (or discovered whatever is causing it). Best advice I can offer with that, should you be willing to test them, is to do a binary search with the versions - try the version halfway between the current one and the one that works, try a newer version if it starts working again, try an older one if it doesn't, repeat.