My iPhone has hundreds of apps occupying 10 GB of space - we'll say that a TB can only store 10K apps, though. A 12 TB drive costs $240, so the cost to store 10K apps is about $20, or about $0.002 for each app stored.
For the $99 Apple charges, they can store 50K apps. There's an estimated 2M apps on the iOS app store - those probably occupy around 200 TB, which Apple could store for about $50K. Could multiply the figure by 3 to allow for backups, but that's probably around what it costs Apple per year, and they collect the fees annually, so that's probably about fair.
You're over simplifying. It's not just one binary + backups.
Developers distribute bitcode versions of their app to the App Store. App store creates device-optimized versions. For example, some devices uses 2x resolution of images assets (for retina displays) while some devices uses 3x resolution (iPhone X for example). Some devices has a 32-bit processor while others have a 64-bit processor so different compiled binaries are needed. Some assets are meant for iPhone only while some are meant for iPad only. Apple creates a binary specific to those device families and only includes assets necessary for a device to run it. This is to cut down the app size.
Essentially, there's about a 10x10 device matrix where 10 different iPads and 10 different iPhones each have their own device optimized binary. A single ~1GB game can end up having ~50-100GB worth of device optimized binaries. Then there's backups, there's previous versions that Apple keeps (which users can download), there's IAP purchases for additional DLC packs like extra levels for games which could be 1-2 GB each, redundant copies stored at edge servers (especially in China where customers can't download from USA servers), and etc...this could amount to several TBs of total cloud storage across all of Apple's servers just for one app.
1TB of S3 from Amazon costs more than $200/year.
On my iPhone, Call of Duty from the App Store is 2.6GB. On my iPad Pro, it's 2.7GB. On my iPad mini, it's 2.6GB. Each device has their own optimized binary.
And that's not even including the app review times that Apple has to pay out to their employees (app reviewers make about $30/hr) or the many services Apple provides developers.