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Folders would be okay to add, it would not increase the memory required by much. But stuff like eShop music and themes are 100% going to slow down the system. It did that on the classic 3DS, it did that on the PSVita (adding a custom background slowed it down), the PS4 menu is really slow with a theme loaded.
Also folders would require additional clicks to go anywhere since the easiest is to press left on the home screen and go to all games.