You must have launched PandoraBox before the reboot of your iPhone, right?
When you launch apps that send notifications, they keep the way to identify you and throw notifications to your phone.
So the answer to your question is : "the code is running on some PandoraBox machine, not on your iPhone".
iOS at its core now has its own multitasking API built in. The only way for an app to even go into the background it has to use these API's, so even poor programming experience still can't ruin things too much (and, with the flip side of that, poor developer experience could make the app while its running use more resources than needed).
All in all - this shouldn't be an issue. Those apps in the tray don't mean they are running - it literally is also a recently used app tray. And again, the background tasks they can do are limited by the backgrounding API, so like audio, VOIP, navigation, uploads, etc.
As far as being faster, have longer battery life, etc - no. At least not on an average. You may feel that it runs different, and yes there may be a rouge app doing something odd, and forcing it closed may help.
But in general, no - this shouldn't affect speed or battery life, unless those apps are currently doing background tasks such as location, audio, uploading files, etc. Otherwise, their RAM state is saved for quicker relaunch, but no processing power is being used.
Best Answer
No, there's no way a regular user can tell the current state of an app.
Apple can change the state of an app at any time depending on a number of circumstances. None of those circumstances should be of any concern to a user.