Honestly, though, is this the 9 millionth thread about SAT vs. ACT?
Sorry, had to say it. :P
I've read that some schools question an applicant if he/she took the test that wasn't "typical" for the region. So, a school MIGHT find it weird that a student from NY took the ACT - a test that most students on the East Coast don't take. Though, schools like HYPS state on their websites that they have no preference for either. Since there is no way to prove the first theory I heard of, I would just go with whatever test better shows your ability (in this case, the ACT). I don't think it's a huge deal.
"I'm getting worried, especially when I see on CB that some school don't report ACT to CB (Villanova, etc.)"
I'm not sure what you mean. Can you explain further, please?