I also saw no dark mode despite multiple reboots. In my case it wasn’t necessary to delete all preferences, this key was enough:
defaults delete com.devon-technologies.agent "NSRequiresAquaSystemAppearance"
I remember that I tried setting it to false at some point after it was mentioned here: Please add Dark Mode - #5 by Mach-7
But I didn’t like the effect then – too many clashing UI elements. I don’t remember if I set it to true again or deleted the key afterwards. Does such a preference key become more “sticky” if you manually change the value? I wonder if DEVONagent was somehow blocked from automatically deleting it when I updated to 3.12.
I also tried deleting the whole preference file to get a clean one for comparison. I didn’t notice any obvious difference aside from missing all my other preferences, so I restored the previous one.