I just upgraded to Audacity 3.1.3 and found that I could not make a keyboard shortcut for the “Label Sounds” plugin unless I deleted a duplicate version of it from the /Users/[name]/Library/Application\ Support/audacity/Plug-Ins folder. That is, once I deleted/disabled the version in that folder (but still had the version within the Applications folder) I was able to make a shortcut for it in the Preferences.
Maybe this is intended behavior, I don’t know. For me it was very confusing. As I tried to get previous plug-ins working I noticed that some appeared in the Tools > Add/Remove Plug-ins … dialog which were not actually present in the Plug-ins folder of the Audacity App “Package” folder. I always closed and reopened Audacity between making changes to the Plug-ins folders, but I didn’t reboot – so maybe that’s why. If I understand correctly, any plugins which I add should go into the /Users/[user]/Library/Application\ Support/audacity/Plug-Ins folder, but I because of my confusion I also started tinkering with the Audacity App “Package” folder. I’m probably doing something wrong in managing these plug-ins, but I just thought I’d mention it.