I have now had time to read through the manual for KeyTweak and it is completely unsuitable. It's a program for disabling / remapping keyboard keys globally (for all applications and all users), rather than disabling a "hotkey" combination within a specific application.
If Microsoft had used just the Winkey as part of this hotkey assignment then it would have been a lot easier to deal with. However, the fact that they've used the Ctrl key means that I obviously can't block that particular key globally (because I wouldn't even be able to copy and paste, never mind continuing to use Ctrl + D in Photoshop as stated as a requirement in my original post).
Anyway, I think I have come up with my own solution (although I've not had time to test it out yet).
I will use AutoHotkey to create a script to block Ctrl + D only when that combination is pressed in Explorer (which is what I have already) but I will put this in its own script by itself. Then, instead of running it as a script, I'll compile it into a executable. This would mean that it would not be affected if I shut down all running AutoHotkey scripts while testing.
To go one step further and ensure that it can't be easily disabled from running at startup (by editing 'run' Registry keys, or by using MSconfig) I will take the compiled .exe and
run it as a background system Service (where it cannot easily be disabled or killed using Task Manager).
That should pretty much ensure that I can rely on it being there, regardless of what I'm doing on the computer.