It's all about shelf space. Walk down a grocery aisle and you see Oreos, Chips Ahoy, Wheat Thins, etc. If you are a new maker of sweet / salty snacks, what would you prefer: your product appear in equal placement with the others (i.e. on a shelf for all to see), or hidden in a cabinet with a generic "food" label on it?
An iPad (or iWhatever) owner's screen is the same as the aisle. Of course, they can put items into folders, but its their own choice, and even then the folders give a representation of what's inside. Plus, if they choose to folder-ize, having done so deliberately they'll more likely remember where to find their favorite periodicals (and that they're there in the first place).
Placing a digital magazine in the Newsstand Store is like placing it in the magazine section of a supermarket. Placing a digital magazine in another category in the App Store is like leaving a jar of peanut butter in the detergents aisle of a supermarket.
However, once the digital magazine is sold, either through the Newsstand Store or the App Store, the shopping experience is forgotten. The item is paid for and placed in one of the customer’s kitchen cabinets. Magazines sold through Newsstand are placed in a logical place, magazines sold through another category of the App Store are not, it is up to the user to place it somewhere they can find it. I like my peanut butter to be automatically placed next to the honey and jelly, I have no need to put it in another cabinet next to the oregano and peppermill.
An iPad (or iWhatever) owner's screen is the same as the aisle. Of course, they can put items into folders, but its their own choice, and even then the folders give a representation of what's inside. Plus, if they choose to folder-ize, having done so deliberately they'll more likely remember where to find their favorite periodicals (and that they're there in the first place).