I got a 3 on 3 of my AP exams and 2 on the other 2 exams so I’m obviously not submitting the scores to colleges. However, my scores still qualified me for the AP Scholar Award (Score of at least a 3 on 3 separate AP exams).
Should I write “AP Scholar Award” under the awards category on the common app? Will the colleges be suspicious of me not submitting my AP exam scores if I add this as an award? Will colleges realize that with 5 AP classes I should have received a better award than the base AP scholar award?
You can list it if you want, but an AP Scholar award is right up the with a Perfect Attendance Medal in terms of value.
I think it could raise flags as to why you are listing the award but not submitting scores. I’d leave it off.
If you were reporting scores, adcoms would see them, know your performance level. They don’t need CB to tell them you got a moderate bar certificate. It seems like a stretch, even when a kid does better.
Kinda like kids who tell they got an award for hours of vol work, just hours, not what they’ve actually done.
Google “new car for perfect attendance in high school”. 
OP, I’d leave it off the application. Even if you got a 5 on all 5 exams, with the number of kids who take AP classes, it is basically a participation award.
I would recommend not including it. It has little impact and would raise questions/uncertainty/confusion.