I think that note-taking programs are better suited for reference materials. Programs such as
NoteBook,
VoodooPad,
Mori, etc, are excellent for storing notes on projects.
My workflow for projects involves using either NoteBook or VoodooPad for all project notes and tidbits learned for reference, and action items in kGTD/OmniFocus. That keeps my action items lean and without distractions.
That's just my opinion. I suppose it depends on the types of projects involved.