Usna AP exam question

Only if you opt to send them, which you might need to do if you're trying to validate certain courses.
Does USNA see your senior year AP Exam scores?
You will test Plebe Summer to learn whether you 'validate' courses. Your AP scores are not taken into account, you still have to test. My son did not report his AP scores, validated out of one math level and declined the 'jump' to the next level math. Good luck to you!
My DS's AP scores were also on his High School Transcript, but the transcript they saw (with his application) just covered his first six (6) semesters (through the end of his Junior year), so there were quite a few more scores to send from the College Board after that. The SAT Code to send scores to USNA is 5809 (Same code for AP scores). The ACT Code to send scores to USNA is 1742.

He'll send more scores after he takes the last round of AP exams to finish up his senior year.
If you look at the USNA website here:
you will see that AP scores are indeed accepted for validation in Chemistry, Mathematics, Economics, English, History, Political Science, Language (only French, German, or Spanish), and Intro Psych.

Send those AP acores!
I don't think they take AP score for Chemistry. DS will have to take the validation tests for Chem 1 and 2. They will take an AP Bio score of 5 to validate biology, this is what is listed in your link above under Chemistry.
Absolutely. Biology is pigeonholed under the Chemistry Department (and that's what the AP test will validate you out of), but validating Chemistry 1 or Chemistry 2 is by test (at USNA) during Plebe Summer. Upper-level Chemistry courses can be validated by having an interview and taking a test, as well.