I don't think 1. is correct. There is a large body of research looking into different dimensions of brain function, and how different conditions impair those functions.
For example, look at the N-back test for working memory. This is popular in the nootropics community, and is widely used in clinical pharmacology research. There are plenty of other tests. Scientists do experiments like "measure how impaired you are on alcohol vs. antihistamines" to compare impairment profiles from different modes of drug action.
You can measure impairment from sleep deprivation, alcohol, etc., so of course you can measure improvement in attention, reaction speed, working memory, spatial reasoning, and so on.
The difficulty with quantifying effects is not that we need to learn about brain function to know how to measure them, it's that nootropics have quite small effect sizes, if any.
I think it's entirely about 2 -- large studies are expensive, and unless your effect size is enormous you need a large study to detect it.