Not a programmer but do have Keyboard Maestro, etc.
Can anyone suggest how I can go about setting-up a key-combination that can automate these steps from a .md document where I select a phrase or word > right click > Services > Select "DevonThink 3: Create a Markdown Document".
A window opens to select the destination for a new subdocument > <Enter>
Since I don't have that app, I can't run it to see exactly what you want. But I have this question: do you use the mouse or the keyboard to do this right now? If you tell me what keys and what menu items you are currently clicking on, I can probably write you a macro and post it of you in this thread. But without the app I really can't do it without more details.
This won't always work, because of a perennial bug in macOS.
Keyboard Shortcuts for Services frequently will not fire if the Services Menu has not been opened since the system was booted.
And – if the Services Menu has not been populated the Keyboard Maestro Select or Show a Menu Item action frequently won't work the first time around.
(Bad Apple!)
The best solution I know of is to use the Select or Show a Menu Item action twice – once to open the services menu – followed by another action to select the desired service.
To open a menu or submenu – leave off the final menu command.