Have rebooted and Dopus has changed its Preferences font-size. Other things I was running picked up the scaling change automatically before the reboot, so it looks like Dopus is not picking up the re-scaling message from Windows, or is choosing not to act upon it dynamically.
I guess this resolves the main problem. I now to do the dirty work and re-scale all the fonts I changed previously, Directory tree, menus, toolbars, file list pane, etc. It's a shame Dopus doesn't have an application-wide font-scaling setting.
Thanks for your help Leo. I'll close this.