terryanne, what is the total storage capacity of your Macintosh HD? That will be found in About this Mac under the Apple Icon in the menu bar in the Storage tab.
ie. Apple Menu > About this Mac > Storage.
App Trap is a free third party app and yes it does only remove associated preference files. I'm sorry if I gave the impression it would remove ALL associated files.
Only a few applications are capable of doing that and caution should be exercised in using such applications, eg. Clean My Mac
The Mac way would be to perform a full search for all of the components of an application using the Finder or another third party app like Find Any File then trash them manually.
Best by far is to always look for an Uninstaller provided by the developer and use that.
As for is App Trap dangerous/harmful? Well I've had it for years and it's never caused a problem although I cant remember the last time I used it.
OnyX like anything that can access your system files should not be used BEFORE you have a viable backup.
This is just being cautious and you will see that they show you a warning that they accept no liability for damage. This is normal and any responsible developer should display such a warning, it's no reason to panic, I've never heard of OnyX causing a problem.
Your last question is complex. Simply reinstalling your macOS may not solve any problems although many people think it will. Essentially all of your files remain the same, except the Operating System files.
To get rid of all your other data (and any conflicts it may be causing) you would need to erase your Macintosh HD completely. This is what is called a Clean Install.
To do this you must first have a full backup using Time Machine or a Clone of your Macintosh HD.
It can be done using the built in Restore partition, accessing Disk Utility, erasing the Macintosh HD, reinstalling the Operating System and restoring you files and applications from Time Machine. Time Machine will offer to do this as part of the process and you can choose at that time which files, folders, and apps you want to reinstall.
As for upgrading the Operating System to say High Sierra or the latest Mojave I recommend you check your third party apps for compatability. Upgrading to High Sierra should be fine but bear in mind it will change the filing system on your device from HFS+ to apples new APFS. I quick online search will tell you what that means eg.
How to Clean Install MacOS High Sierra