Junior and Senior Year Schedule. Is study hall non-advantageous/Any tweaks anyone would suggest?

I just recently turned in my course selection form, but I can always change it:

AP Latin
AP Chemistry
AP US History
AP Language and Composition
Honors Precalculus
Honors Wind Ensemble
Study Hall

For Senior year I plan on:

0 Period (before school) Bible class (I go to a Christian school so I need another bible credit to graduate)
AP Biology
AP Lit
AP Music Theory
AP Calculus BC
Either AP Stats or Honors Physics (no ap physics at my school)
Honors Wind Ensemble
Study Hall

My goal is to major in Mathematics at MIT or Pre-Med at Johns Hopkins. I’m worried study hall won’t look very appealing to admissions officers, but I feel it’s necessary so I can maintain an exceptional GPA. At the same time, I also want to remain a competitive applicant. Are there any tweaks or suggestions anyone would have on my schedule?

I’m sure there are some admitted who had a study hall in their senior year.
You can tell you can’t get both. It’s either competitive schedule or higher GPA. You can contact admissions officers and ask them which they prefer. If you don’t want to do that, research the schools and what they deem to be most important to an applicant. Start from there and decide on your final answer!
In the end, at those higher tier colleges, officers want to see a competitive schedule and a high GPA, but that is hard to achieve at times.

Study hall is wonderful. At my school study hall is required when more than 3 APs are on the schedule.

Honestly, study hall can be the difference between an 89.67 B+ or a 92.20 A- in a class.

What class would you put in place of the study hall if you were to change it to something else?

I would have an actual class, but nothing too tough that you can’t handle it.

Your schedule looks fine and you can keep the study hall considering you have 4 Ap’s each year, although if your school offers a fun “no/little hw” class such as home economics or shop, you should feel free to take it.
Senior year: take Honors Physics, not Stats. First, Physics is one of the three sciences you’re “supposed” to have. Second, AP Stats is an “AP Lite” for strong students who can’t or won’t take calculus -clearly not your case.