TL;DR - Organize with folders to improve your dev/debug/maintenance efficiency. It won’t affect the performance (run speed) of your game.
I didn’t say it in my last post, and I should have.
Using folders is about being organized and improving your ‘development efficiency’, ability to debug, etc. It has nothing ( * ) to do with how fast your game will run.
I do think it is a terrible idea to put 300 images in the same folder as main. (I don’t even like putting icons in that folder and I was very happy when we could stop doing that for iOS.)
I would put them in a folder called images and I would also probably organize them in sub folders by general category. Perhaps: ‘images/interface’ and ‘images/game’. You need to develop your own org style that is meaningful to you you.
Again, this is really just about being organized in your development, debug, and maintenance.
* So, why an asterisk? When one makes an absolute statement, there is always a scenario where you are wrong. From my past experience with a dozen plus operating systems, there are scenarios where the OS performs better or worse when looking up files. In some cases having too many files in one folder is a big negative. In others, having really long filenames is a negative.
Having said all that, iOS and Android (as well as Windows and OS X) are modern OSes. They do not suffer from any limits you could possibly hit with your game. By the time you hit those limits, your game would be too big for mobile and really huge as a desktop game.