I reported this potential issue to the support address, however...
I see that my registration key is indeed present in the correct
directory:
~/Library/Group
Containers/G69SCX94XU.duck/Library/Application Support/duck/
-rw-r--r-- 1 username staff 679 Aug 23 2020
n[omitted].cyberducklicense
In my case, the "duck" command was installed via MacPorts, and
it appears there may be some disparity between how this works vs.
the GUI-based application.
In MacPorts, we have the bundle installed in:
/opt/local/libexec/duck/duck.bundle/
I do not see any configuration file or setting that may indicate a
different Application Support location, one would presume that the
CLI would simply refer to the correct location on MacOS. Perhaps
this is a bug or oversight?