Some applications and utilities come with extended facilities to view and manipulate files, regardless their visibility status. The app cannot do anything to prevent this situation (as any other app that we are aware). A fairly simple way to prevent an item to appear in the Spotlight results is to include the item in a folder excluded from Spotlight searching. Here's how to do it step by step.
- Open Spotlight (You can use Spotlight to find himself).
- Go in the "Privacy" panel.
Click the "+" button to add a folder that you do not want to appear in the Spotlight results (for secrecy reasons, it would be better not add directly the folder you hide, but simply a folder that contains among other items also it).
- This is all. The folder and all its contents will no longer appear in Spotlight.