Ubuntu 18.04 VM freezes and kills single ESXi when cloning disk

Assuming there is no there are no connectivity issues between the ESXi host and the storage device and you already checked if there are no path inconsistencies to the LUN (if the case), it appears you have a driver compatibility problem caused by ESXi patching.

You could try to disable the vmw_ahci driver:

esxcli system module set --enabled=false --module=vmw_ahci

If that does not work, you should revert to the previous patch of ESXi or try to restore the initial drivers (which may be quite difficult).

Also, checking the vmkernel.log, vobd.log and vmksummary.log may reveal details about the exact cause.

This one was stupidly simple: One hard drive failed which was accessed by this very VM as a data disk. It was physically broken but neither ESXi nor the management board saw that.

TL;DR: A HDD failed but that was not detected. This issue was not software related.