Why did Itsuki only get 4 subject scores? Did she literally skip one? If so, why? Is it possible to tell which one based on Japan's rule for listing scores?
Most probably literally skipped one. In Japan, the actual test is (mostly) prepared by each university. That is, different tests for different universities. Which subjects to be included is also a decision on the university side. So, when a student applies to a university requiring fewer subjects, s/he will take those practice tests with fewer subjects.
According to Futaro's card, you need an above 54.8 deviation to be graded D. Itsuki's is 48.7. How did she get a D? Maybe she should get F?
As indicated above (and commented), it depends on the university. From the scene, you can tell the university Itsuki is going to apply is easier to get in. (Roughly, you can think this way: if the university on Futaro's card is Harvard, the university on Itsuki's card is a lower-ranked one)
How are their deviations calculated? What statistics can be deduced using those on their cards? (Just for your convenience, Itsuki's ranking is 176598/234516.)
It is called Hensachi. According to the article, it is calculated with:
- A x { (Score - Average Score) / Standard deviation } + B,
where A=10 and B=50 (In SAT, A=100 and B=500). Hensachi/deviation-score 50 means one got the average score, so Itsuki is slightly less.