tl;dr It’s worth having ‘notes’ and ‘todos’ separately, probably in separate apps. They are too different.

If you search for ‘productivity tools’ being used in a wild, you usually see apps for note taking/making. But it often comes in pair with some todo-lists app.

For me it feels the reason is - vastly different lifecycles: there are ‘notes’, made as a ~long-term thing; and ‘action items’, a ~short-term things to execute.

For last 5 months I’ve being using zettelkasten-like approach for making my notes, and as an experiment I’ve tried to keep my todo lists in the very same manner.
And it wasn’t as smooth as I’d want it to.
The usage of notes and todos drastically differs - the way you add, search, modify, get rid of them.

You often add and remove the todos, making tons of them in the process. A low level action planning. Creating again and again until it is done.
Notes are produced not that often, usually much more lengthy, interconnected, not necessarily sorted in any sequence of sorts, prone to be changed again and again.

Having todo lists in separate flow, treated differently - is just a breeze of fresh air.

For me a combination of the archive for notes and taskpaper for todo lists works nicely. Hotkeys and automatization for the win!

On the other hand vim + vimwiki + vim-zettel is really great, in some aspects (searching for existing notes in place) is just awesome.
Also taskwarrior looks promising. It’s being years since I’ve heard about it, yet haven’t fully checked out.