Searches only use a criterion to limit the items returned by a search if that criterion is both currently showing and checked. The only exceptons are items normally hidden in the Finder because they are invisible or inside packages.

If these criteria are not available (that is, not visible in the window), searches will only return items normally visible in the Finder. That means invisible items and items inside packages are not found. Therefore, to do a search that returns every item without exception, add the Visible criteria to the window, check the box to search inside packages, and leave all other criteria unchecked.