My hr beats much faster due to pectus excavatum, do i burn more calories when exercising because of this?

Most likely not: It is difficult to determine how many calories you are burning during exercise on heart rate alone. The only accurate way to determine calorie consumption is with testing such as a calorimeter. But keep up the exercise, its all beneficial regardless of how many calories you burn. The benefits far exceed calories burned.

Calorie burn: Generally, you burn more calories when your heart beats faster. Since your heart may be working harder due to compression from pectus excavatum, make sure you have received the okay from the cardiologist before progressing with exercise.