There are Xposed modules that can really mess up the look of the phone. (The damage isn't permanent, because the whole idea of Xposed is to change things at run time, not in the apps as they're stored in the phone.) But about the worst you can do with Notify Clan is kill notifications you really do want, and that's as easily fixed as just turning that notification off in Notify Clean, or unchecking Notify Clean and not blocking any notifications at all.
I haven't found anything you can permanently ruin with an Xposed module - Xposed doesn't work that way. (At very worst, you uninstall the module, then uninstall Xposed, and you're back to where you were when you started.) It's not like rooting or flashing a ROM, that can brick the phone or leave permanent marks. If you don't like what Notify Clean does, turn it off (uncheck it). But if you like what it does, look at the Xposed site and you'll find a lot of modules for things you may never have thought of, that might be nice to be able to do. And, again, none of them make permanent changes to the phone, they just change the program when it's running. (The app sitting in storage, which is what gets loaded every time you run the app, never gets touched.)