My opinion is that this has nothing to do with the Sonnet or NVMe drives. It's the way of how macOS manages the devices in PCIe slots, because if it was duo to mounting issues, there will be unmounted but present drive.
So here is my experience:
In slot 6 I have StarTech PCIe to NVMe U.2 adapter and connected to it is Micron 9300 Pro 3.84TB drive (Storage, APFS)
View attachment 2340139 View attachment 2340140
Last few days, on Sonoma 14.2.1 I had messeges like this, sometimes on cold boot, sometimes after restart:
View attachment 2340138
After that message, there is no drive mounted or drive present as a device at all in the system
2 days ago, I have installed Sonoma 14.3 and problem disappeared. Let's see for how long.