Disk (EXT4) suddenly empty without any sign of why
Solution 1:
I cannot guess how that happen.
But to "wipe" a disk "clean", the fastest way is deleting the partition and recreating the partition. You can get a "clean" "formatted" EXT4 partition that way in just a few seconds.
If somehow root escalation is used, that is one way to do it.
Solution 2:
Restore your backup from the time before the data-loss, and restore last night's backup. Compare the two.