If you have a well-oiled system for taking notes, I wouldn’t change it other than perhaps adding a JD number to the note title. If you think it’ll help.
If I want to do that in a non-disruptive way I’ll generally do it in square brackets at the end:
Title of my really great note [23.03]
This post might help with the ‘where to store these things’ question.
Your option 2. is where I’d be leaning. Use each technology for what it’s good at, and use my system to know where all the things are.