By the power of truth, I, while living, have conquered the universe.
You answered your own question...
Onyx was destroyed when Kurt detonated the FENRIS warheads, the planet split apart into the trillions of Sentinels that formed it. All that's left of Onyx is the Micro Dyson Sphere, it's 3 meters in diameter and is encased in a slipspace bubble of compressed dimensionality. Did I mention that said pissed off Sentinels will shoot anything that comes anywhere near it?
Don't tell me they just formed back together again. Even if they did, an atmosphere and habitable surface won't just appear out of nowhere.
Read the final Terminal, Mendicant Bias tells John he's sending him to the Forerunners to prove he's atoned.