This was still drifting through my mind today, so I tried it out.
I was able to quickly change the keyboard shortcut using a feature of KeyCue.
Just in case it was a KeyCue only thing, I also repeated this change subsequently with the more tedious keyboard shortcut settings in system settings - so you don’t need a special app to do it.
After that, while the warning mesaage on the action still shows up on the action’s properties, Drafts does then assign it to the action (as can be seen in the menu entry for the action - below), and I can confirm, does run it on pressing ⌘+N.
Personally I would not choose to override the new draft keyboard shortcut, but if you really wanted to, then you could.
… and I’ll be able to sleep peacefully tonight now I’ve got that niggly question out of my head. 