No they aren't. Locked down restrictive app stores are the problem. App stores can provide visibility to apps that might not get it otherwise. Or help developers reach an audience through a central deployment platform. They can promote better security as well. Making updates easy and prompt. They're more or less at the heart of every Linux/BSD platform for a reason.
Let's be honest. How frequently do you check for updates to every program you installed manually? Even if the program itself notifies you. Are you going to navigate to the website immediately. Find the download link and promptly install for every, single, one. App stores and repositories are literally one of the greatest software inventions of the last 30+ years.
Being locked to a specific store or repository is the problem. Which is why everyone but apple tends to provide solutions. Whether it's side loading, flatpack, app images etc.