Applications are able to start back up on their own. I have been able to get familiar with what apps start right back up, by themselves, and what apps do not in my device specifically... I also have learned that hibernating or force closing some other apps, especially apps in which you don't have much knowledge about can cause certain features on your device to stop working until the app is either restarted or the device is restarted. On Motorola phones for instance, if you hibernate or stop the "Moto" app, your gestures to quickly turn your flashlight on and off, or the gesture to quickly open your camera with two flicks of your wrist will cease to work if you hibernate or force stop this "Moto"app. My best advice is to familiarize yourself as much as possible with what you're hibernating and force closing because more likely than not, an application you are hibernating is causing whichever issue you're blaming CCleaner for.
You can always go by trial and error by checking to see if you still have the same issues by not hibernating/force closing specific apps to check and see if any app your closing is causing all or any of your headaches.