I want my Mac (running macOS Sierra), to stop hiding Dock when I enter Command + Option + D.
I need to use that key command for InDesign.
One other possibility is to remap the shortcut in InDesign to something else.
You can do this by going to System Preferences > Keyboard > Shortcuts > App Shortcuts. Add a new shortcut. Select the InDesign application, the shortcut you want to use, and the menu bar item which this shortcut will trigger when you press that key combination in InDesign (this will only work if you have a menu bar option for whatever you want to trigger).