How inappropriate is it to track semi-secret information using paper or other memory aids?
There's two schools of thought on this subject - one is that you can do anything unless the rules say you can't, the other is that you can only do what the rules say you can. I believe there's a better argument for the second case, because the rules are generally written to define the game, and can't expressly prohibit everything you might try to do. The rules of Catan don't specifically say you can't look through the Development Card deck, but I don't think anyone would consider that fair play. By-hand tracking is never mentioned in the rules, so I don't think it should be included. 

In my opinion, a board game should be one person's brain and luck against the other's. Would it be fair to run an app computing my odds of winning a Risk battle? Or compute my chance of drawing that straight flush in a poker game? These are things I could figure out myself if I had the time and math skills, but are much easier with an aid. Similarly, tracking resources could be done with a good memory, but augmenting that with paper and pencil doesn't seem right.

TL;DR: I would consider by-hand point or resource tracking at best unsporting, and at worst, against the rules.