I have got to ask. What was the domain? Why were these files so important?
Related… I think three things are missing from this conversation: context, scale, and cost.
If you’re doing work that may have legal or historic implications (and I suppose anything could have either of those eventually—the world is a weird place), you should be taking scalable, sustainable stewardship into account.
Scalable means “Does this organizing approach still work if I have orders of magnitude more items than I currently have?”
Sustainable means “Will this still work in 20 years, with whatever technology we might have?”
Stewardship means “Will this work for others, if I have to get someone else to work with this?”
This is where context comes in. Many of my notes are just for me, so I’m not so worried about these questions.
And finally, this is where cost hits. Any organizing schema has two kinds of costs: input (storage) and output (retrieval). The more rigorous and complex a system is, the more likely it will be costly to file something away. However, it’s also likely easier—less costly—to retrieve it. For your average “note-taker,” balancing these two costs is going to be paramount.