Fewer than 1% of the apps in the store will have any effect whatsoever on Apple's hardware sales. Easily 99% of apps are long tail products that don't influence prior decision-making.

AS for margins, once you factor in Apple's high spending on R&D and engineering, their margins are fairly normal. Apple are financially successful because they sell high quantities and don't chase the extreme bottom of any market. Notice for example how they don't (currently) offer any mainstream external displays.