The installation where the problem first occurred was 7.9.16. I updated java to latest version and Ignition to 7.9.21., but the problem persists. I also specified the wrapper.java.command path in ignition.conf file, but that didn't help.
Are you sure that OPC UA module is the one from the 7.9.21 install? That would be the only obvious reason for the missing libraries. Consider stopping, clearing out user-lib/modules, and re-installing.
Thank everyone for their answers. We diagnosed the problem: antivirus.
Since 9th of February, Bitdefender definitions recognize JobSupport class located in file __456175499__opc-ua-server-4.9.21-all.jar as a trojan.
Bitdefender removed this class from the file, but not the file itself (so the file was not repopulated after GW restart).
Disabling the antivirus, stopping GW, deleting xopc cache and restarting the GW fixed the problem. Although, an exception is yet to be implemented in Bitdefender to ignore Ignition folder, which proved to be a bit difficult.