I attend a high school in Ontario and have to choose my classes for IB for next year (11th grade).
I want to study astrophysics in university but my school doesn’t offer Math or Physics at the higher level in IB. I have to take english and economics/history at the higher level (and I am taking Chem HL too).
Will elite colleges in the US hold it against me that I didn’t take math and physics HL? Should I self-study for ap exams to make up for it (AP Calc BC, AP Physics 2, etc)?
US colleges don’t care what classes you took as long as they’re the hardest available. They’re not going to fault you for not taking a class if it wasn’t offered at your school.
As for self-studying for the APs, that’s up to you, but if you do poorly on them or your grades in IB suffer as a result, then they’re a bad idea.
Thank you for your reply. 
I’ll see next year if I can manage the course load and self-studying ap. I’m just worried that I’ll be at a disadvantage if and when I get to college.
Pamajo Education offers online IB courses so perhaps consider asking your IB coordinator about whether you’d be able to take HL maths on there. A friend of mine takes a language ab initio course on there and has no complaints about the interface or classes. But to do well in this online class (and in the final exam) you’re going to have to be an extremely self-disciplined student as you’ll be assigned work for the week and you’ll need to organize your time to complete all the work before the due date. Sounds easy but trust me it does get hectic.
Here’s the course: http://www.pamojaeducation.com/IB-online-courses/mathematics-hl.asp
And no, no college will penalize you because your school doesn’t offer HL physics or maths. Just make sure your guidance counselor mentions this somewhere. Does your school not offer SL physics? If they don’t, instead of self studying APs consider taking a regular physics course (during the school year or in the summer) - it will make things for you so much easier. The IB diploma as is is very busy so self studying APs will make the experience all the more difficult/hectic.
Thanks for the link. My school only offers SL physics (no HL). And I can’t take a regular course. I have to do the full IB diploma–we can’t mix and match IB and regular. I’m going to take 12th grade Bio during summer and stick with Chem HL and Physics SL during the school year. I’m reconsidering self-studying AP; seeing as the IB workload is already crazy, I’d rather devote time to some meaningful ecs that I love rather than piling on the academics.
Out of curiosity, how much of a commitment would it be to self-study AP Calc BC or AP Physics? Would an hour a day for 4-6 months be enough?