No. Actually it’s because the curriculum of an AP course is not designed to prepare one for a Subject Test. As you correctly note:
AP courses are designed to be equivalent to a college course, and as such, cover the topics in less breadth and more depth. Now some schools/teachers might spend time filling in the gaps, but really the onus is on the student in this case.
No. Many elite universities have made then “optional” or “recommended” (as has Georgetown), but that does not mean that one should not submit. There is a whole discussion here:
http://talk.collegeconfidential.com/college-admissions/2027962-sat-subject-tests-are-not-truly-optional-for-middle-upper-middle-class-applicants-at-elite-colleges-p1.html
Anyway, for the OP’s original question, I think the discussion is moot until you actually take the Subject Tests and have scores. A score in the high 600’s will not mean an automatic rejection. But in general, I would suggest submitting 3 tests.