My overall average was above a 90, but the way it works at my school is you don’t get honors unless you have at least an 85 in every class. I had two classes below 85, so I didn’t get honors. Do colleges care?
Affect 
I’d be less concerned about honor roll and more concerned about the grades you have in each of your classes. Colleges will see your transcript-- they’ll know that you did well in the courses you did well in and that you did less well in the courses you did less well in, and that tends to be more valuable than blanket achievements like honor role, though GPA is an important piece of the puzzle.
Colleges generally do not get grades in %, only in letter grades. So, you won’t have to worry about the honor roll. IF you DID have it, it would be a nice addition to add to your application, but it’s not a huge deal.
So, not making honor roll will not AFFECT you that much. The EFFECT of not having honor roll is small as long as your letter grades are good! (by the way, I’m just trying to say that affect is a verb, and effect is a noun)
Thanks!