I’ve been using it since it was in Beta, and have never had that happen.
That said, I have less than 100 apps, and I review every item carefully before deleting.
One thing I like about Clean My Mac’s deletion tool for apps is that it cleans up the scattered bits and pieces.
You could always use Clean My Mac to generate a list, which you manage manually.
Alternatively, you could create a folder in Apps called Closet, where you move apps you are thinking about deleting, then check it at some pre-determined interval to actually delete those you haven’t missed.