App Stores have a lot of problems that push developers away from them:
1. Apple have a history of convoluted review processes and arbitrary rejections. It has a terrible reputation amongst devs.
2. Thanks to unpredictable reviews you can't time when a new upgrade becomes available to coincide with e.g. website changes, emails.
3. The App Store can't upgrade apps whilst they're running.
4. App Store 30% standard cut is far too high when a developer could sell direct from their website and pay 2% or less to a card processor.
5. The App Store UX is itself pretty bad. There's no flexibility or ability to customise how your app appears.
6. Devs are forced to allow app reviews and ratings although they may not wish to have that e.g. because users use reviews as a way to request support instead of an actual support system, but you can't reply.
7. App Stores often create problems for corporate or managed desktop deployments.
8. For software that is billed, despite exhorbitant fees their billing engines can be primitive. For instance even years after launch the Windows app store had no ability to do bulk discounts or other kinds of completely normal retail strategies. I don't know if it does these days, but I do know of an app developer who shipped via the WAS and whose business was badly hurt by Microsoft's lackadaisical attitude towards basic features like that. They could have sold big into education but couldn't get much traction because there was no way to offer reduced rates to schools.
9. App Stores enforce random policies unrelated to the core mission of app distribution. For instance the Mac App Store is extremely vague about to what extent plugin mechanisms are allowed. Good luck implementing an IDE or browser in the MAS; you'll always be living in a grey zone. It also forbids any kind of custom licensing mechanism or copy protection, so when Apple's is insufficient you're SOL and requires all languages to be in the same bundle yielding huge downloads (=lower conversion rate due to failed downloads). Those are just implementation limitations but you aren't allowed to do better.
Basically, Apple don't have a good track record of creating an excellent developer experience with their app stores. On mobile they forced devs into it against their will. On desktop where backwards compatibility prevents it, devs have nearly universally rejected app stores ... even when an app is in it, it's common for websites to direct users to their own distribution points.