I create a lot of markdown files, so a keystroke method would be useful. I created an application specific shortcut through system settings. The shortcut shows up in the menu, and system settings does not show a conflict, but the shortcut is not working.
Any suggestions? I have no problem using AppleScript (if I don’t have to write it) and I own Keyboard Maestro.
I just set an app-specific shortcut of Control-M and it works as expected. Try it.
Worked. Thanks! Must have been a problem with my choice of keys.
No problem.
I was coming up with all sorts of hoop-jumping solutions to this and you ruined it. 
An app-specific shortcut it is, thanks!
Occam’s Razor, my friend. 
A riff on Jim’s suggestion.
If you have a Markdown document, or any type of document, that you want to use as a template or starting point for new documents then:
This special naming syntax will cause DEVONthink to recognize ⌘^M as the shortcut to create a new document using My Template as the starting point.
Note: there are three underscores before “Cmd”. Those are required to make this work. Make up your own file names and shortcuts, mine is just an example. You can refactor that shortcut in KeyboardMaestro macros, or for TouchBar keys, etc.
Oh yes, helped me too 
As I want to have a shortcut to create a new md document from a template, I was happy to find this. But alas I it doesn’t work for me. I tried a couple of different shortcut commands, in the case that that was the problem, and still no luck. Any ideas…? If I understand correctly @BLUEFROG suggestion, that involves assigning a shortcut to services in System preferences, which would not work for creating a shortcut to a template…? Thanks for any help!
The post you quoted was for DEVONthink 2.x, several years ago.
You are correct, however, the feature seems to have disappeared in DEVONthink 3. That’s unfortunate, it was very useful.
@BLUEFROG @cgrunenberg was the ability to name a template something like “My Template___Cmd-Ctrl-T” removed or is there a glitch?
This shortcut is already used by another menu item.
If a shortcut is used by DEVONthink (as @cgrunenberg wrote), then in general it should be possible to
Didn’t test with templates but I think it should work.
Take a look at CustomShortcuts app, it’s easier to use than System Preferences as it features auto completion.