One of the fastest ways to hide a file or folder, from Spotlight, on the fly is to add the .noindex extension to the end of the filename or folder. The simplest way to get those files hidden is to create a folder, preferably named something innocuous, and add the extension to the end of the name. I’ll end up with a folder named “Nothing to See Here.noindex” or something similar.
Hide just a single file
Select the file to be hidden. Right-click and select Get Info, or click Command+I. Find the Name & Extension field, and replace the current extension with .noindex. When prompted to confirm that I want to change the extension, I agree. Now my file is properly hidden from Spotlight search.