It seems that you are mixing up some terms:
Matter = integration in the Apple Home ecosystem and app, which uses Thread as communication protocol.
Remote Access via Thread = remote access for the Nuki app via Thread
Remote Access via WiFi = remote access for the Nuki app via WiFi
In your case remote access via Thread was not available and the Smart Lock fell back to WiFi. The remote access via Thread option is only available if it is supported by the thread border router. In order for the Smart Lock do find out if it is supported by a router, it has to try it out. This is always done with a certain logic after a reboot.
AppleTVs and Homepods in general support remote access via Thread, but sometimes they also stop providing this service to the Smart Lock. In this case the Smart Lock might fall back to WiFi or stop providing remote access at all.
What happened in your case is that the Smart Lock rebooted after the FW update and that your Apple hub currently provides remote access via Thread and therefore the Smart Lock is also using it. If it is slow or unstable, just turn off remote access via Thread and keep using WiFi.