Is it too much paranoia to be suspicious of software that require a separate "Helper App"? I was out trying to find a good system monitor application and decided to give a shot to Monity, which has gotten several good reviews from respectable journals. 

What bothers me is that the application that comes from the App Store is only a portion of the software. The software asks for download of a so-called Helper App for free, in order to get additional panel (which would be what I am after essentially). 

There is little to no documentation why this helper app is required and the fact the fact that a portion of the software doesn't go through Apple's control doesn't give me any good vibes. 

I know that Apple has certain hinders that prevent developers to reach system resources, but in most cases I have seen at least some explanation to what the helper contains by the developer. In this case there is no information on the dev homepage and I didn't get a reply to my email to the developer. 

So the question is: What specific controls do apps go before they are on App Store? In other words, why would a dev choose not to deploy his/her program (or parts of it) on the App Store?
All applications sold through Mac App Store have to be sandboxed. Being in a sandbox restricts what the application can do quite a lot. For example they can not access files in folders to which you did not grant them access explicitly via the system Open File dialog. The complete sandbox documentation can be found on the Apple Developer pages, but the important thing to note is that it is very restrictive. 

Having a system tool that can live in it is near impossible. Also note that Apple itself does "cheat" when it comes to the sandbox rule. For example the XCode is accessible via Mac App Store but it is not sandboxed (because it wouldn't work if it were). 

In general though, sandboxing is a good thing. The only way to be really sure if an app is behaving well or not is to see if there were complaints or signs that the developer can not be trusted. Note, however, that before the Mac App Store existed all applications were distributed via other channels and most of the time things went fine.