I do create a new text file each time, although it's sort of arbitrary what I group. Sometimes I will put my entire day's notes for a given book in one file. Other times I'll have atomic notes for each thought.

The organization process is wholly dependent on how much I come up with in a day/week. I mostly read for fun now, so I don't have to rigorously organize lecture notes or anything like that for later use. On the other hand I'm pretty rigorous with how I process tasks. As a ballpark figure I'd say 30-60 minutes per week, or 5-10 minutes per night.

To your latter point, I think that's fair. The main idea is to be flexible and recognize when you need new categories or whatever (and when you can dump unhelpful ones).