.DS_Store files aren't important system files, they're files made by Finder that keep track of window and icon positions for the folder the .DS_Store file is in. Feel free to delete them, the worst thing that could happen is your desktop icons reset their positions. They reappear anyway, with default icon/window settings (I'm STILL trying to make some kind of script that deletes all .DS_Store files because of all my messed up window sizes and positions 😟 )
Anyway, open up OnyX (click Cancel for the Verifying Startup Volume popup), type in your password, click Parameters, then Finder, and uncheck "Show hidden files and folders".